Pufa polyketide synthase systems and uses thereof

ABSTRACT

The invention generally relates to polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) systems, to homologues thereof, to isolated nucleic acid molecules and recombinant nucleic acid molecules encoding biologically active domains of such a PUFA PKS system, to genetically modified organisms comprising PUFA PKS systems, to methods of making and using such systems for the production of bioactive molecules of interest, and to novel methods for identifying new bacterial and non-bacterial microorganisms having such a PUFA PKS system.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a Continuation of U.S. application Ser. No.11/676,971, filed Feb. 20, 2007, which is a Continuation of U.S.application Ser. No. 10/810,352, filed Mar. 26, 2004, now U.S. Pat. No.7,211,418, which claims the benefit of priority under 35 U.S.C. § 119(e)from U.S. Provisional Application Ser. No. 60/457,979, filed Mar. 26,2003, entitled “Modification of a Schizochytrium PKS System toFacilitate Production of Lipids Rich in Polyunsaturated Fatty Acids”.U.S. application Ser. No. 10/810,352 is also a continuation-in-part ofU.S. patent application Ser. No. 10/124,800, filed Apr. 16, 2002, whichClaims the benefit of priority under 35 U.S.C. § 119(e) to: U.S.Provisional Application Ser. No. 60/284,066, filed Apr. 16, 2001; U.S.Provisional Application Ser. No. 60/298,796, filed Jun. 15, 2001; andU.S. Provisional Application Ser. No. 60/323,269, filed Sep. 18, 2001.U.S. patent application Ser. No. 10/124,800, supra, is also acontinuation-in-part of U.S. application Ser. No. 09/231,899, filed Jan.14, 1999, now U.S. Pat. No. 6,566,583. Each of the above-identifiedpatent applications is incorporated herein by reference in its entirety.

This application does not claim the benefit of priority from U.S.application Ser. No. 09/090,793, filed Jun. 4, 1998, now U.S. Pat. No.6,140,486, although U.S. application Ser. No. 09/090,793 is incorporatedherein by reference in its entirety.

FIELD OF THE INVENTION

This invention relates to polyunsaturated fatty acid (PUFA) polyketidesynthase (PKS) systems from microorganisms, including eukaryoticorganisms, such as Thraustochytrid microorganisms. More particularly,this invention relates to nucleic acids encoding non-bacterial PUFA PKSsystems, to non-bacterial PUFA PKS systems, to genetically modifiedorganisms comprising non-bacterial PUFA PKS systems, and to methods ofmaking and using the non-bacterial PUFA PKS systems disclosed herein.This invention also relates to genetically modified microorganisms andmethods to efficiently produce lipids (triacylglyerols (TAG), as well asmembrane-associated phospholipids (PL)) enriched in variouspolyunsaturated fatty acids (PUFAs) and particularly, eicosapentaenoicacid (C20:5, ω-3; EPA) by manipulation of a PUFA polyketide synthase(PKS) system.

BACKGROUND OF THE INVENTION

Polyketide synthase (PKS) systems are generally known in the art asenzyme complexes derived from fatty acid synthase (FAS) systems, butwhich are often highly modified to produce specialized products thattypically show little resemblance to fatty acids. It has now been shown,however, that polyketide synthase systems exist in marine bacteria andcertain microalgae that are capable of synthesizing PUFAs frommalonyl-CoA. The PKS pathways for PUFA synthesis in Shewanella andanother marine bacteria, Vibrio marinus, are described in detail in U.S.Pat. No. 6,140,486. The PKS pathways for PUFA synthesis in theeukaryotic Thraustochytrid, Schizochytrium is described in detail inU.S. Pat. No. 6,566,583. Finally, the PKS pathways for PUFA synthesis ineukaryotes such as members of Thraustochytriales, including the completestructural description of the PUFA PKS pathway in Schizochytrium and theidentification of the PUFA PKS pathway in Thraustochytrium, includingdetails regarding uses of these pathways, are described in detail inU.S. Patent Application Publication No. 20020194641, published Dec. 19,2002 (corresponding to U.S. patent application Ser. No. 10/124,800,filed Apr. 16, 2002).

Researchers have attempted to exploit polyketide synthase (PKS) systemsthat have been described in the literature as falling into one of threebasic types, typically referred to as: Type II, Type I and modular. TheType II system is characterized by separable proteins, each of whichcarries out a distinct enzymatic reaction. The enzymes work in concertto produce the end product and each individual enzyme of the systemtypically participates several times in the production of the endproduct. This type of system operates in a manner analogous to the fattyacid synthase (FAS) systems found in plants and bacteria. Type I PKSsystems are similar to the Type II system in that the enzymes are usedin an iterative fashion to produce the end product. The Type I differsfrom Type II in that enzymatic activities, instead of being associatedwith separable proteins, occur as domains of larger proteins. Thissystem is analogous to the Type I FAS systems found in animals andfungi.

In contrast to the Type I and II systems, in modular PKS systems, eachenzyme domain is used only once in the production of the end product.The domains are found in very large proteins and the product of eachreaction is passed on to another domain in the PKS protein.Additionally, in all of the PKS systems described above, if acarbon-carbon double bond is incorporated into the end product, it isalways in the trans configuration.

In the Type I and Type II PKS systems described above, the same set ofreactions is carried out in each cycle until the end product isobtained. There is no allowance for the introduction of unique reactionsduring the biosynthetic procedure. The modular PKS systems require hugeproteins that do not utilize the economy of iterative reactions (i.e., adistinct domain is required for each reaction). Additionally, as statedabove, carbon-carbon double bonds are introduced in the transconfiguration in all of the previously described PKS systems.

Polyunsaturated fatty acids (PUFAs) are critical components of membranelipids in most eukaryotes (Lauritzen et al., Prog. Lipid Res. 40 1(2001); McConn et al., Plant J. 15, 521 (1998)) and are precursors ofcertain hormones and signaling molecules (Heller et al., Drugs 55, 487(1998); Creelman et al., Annu. Rev. Plant Physiol. Plant Mol. Biol. 48,355 (1997)). Known pathways of PUFA synthesis involve the processing ofsaturated 16:0 or 18:0 fatty acids (the abbreviation X:Y indicates anacyl group containing X carbon atoms and Y double bonds (usually cis inPUFAs); double-bond positions of PUFAs are indicated relative to themethyl carbon of the fatty acid chain (ω3 or ω6) with systematicmethylene interruption of the double bonds) derived from fatty acidsynthase (FAS) by elongation and aerobic desaturation reactions(Sprecher, Curr. Opin. Clin. Nutr. Metab. Care 2, 135 (1999);Parker-Barnes et al., Proc. Natl. Acad. Sci. USA 97, 8284 (2000);Shanklin et al., Annu. Rev. Plant Physiol. Plant Nol. Biol. 49, 611(1998)). Starting from acetyl-CoA, the synthesis of docosahexaenoic acid(DHA) requires approximately 30 distinct enzyme activities and nearly 70reactions including the four repetitive steps of the fatty acidsynthesis cycle. Polyketide synthases (PKSs) carry out some of the samereactions as FAS (Hopwood et al., Annu. Rev. Genet. 24, 37 (1990);Bentley et al., Annu. Rev. Microbiol. 53, 411 (1999)) and use the samesmall protein (or domain), acyl carrier protein (ACP), as a covalentattachment site for the growing carbon chain. However, in these enzymesystems, the complete cycle of reduction, dehydration and reduction seenin FAS is often abbreviated so that a highly derivatized carbon chain isproduced, typically containing many keto- and hydroxy-groups as well ascarbon-carbon double bonds in the trans configuration. The linearproducts of PKSs are often cyclized to form complex biochemicals thatinclude antibiotics and many other secondary products (Hopwood et al.,(1990) supra; Bentley et al., (1999), supra; Keating et al., Curr. Opin.Chem. Biol. 3, 598 (1999)).

Very long chain PUFAs such as docosahexaenoic acid (DHA; 22:6ω3) andeicosapentaenoic acid (EPA; 20:5ω3) have been reported from severalspecies of marine bacteria, including Shewanella sp (Nichols et al.,Curr. Op. Biotechnol. 10, 240 (1999); Yazawa, Lipids 31, S (1996);DeLong et al., Appl. Environ. Microbiol. 51, 730 (1986)). Analysis of agenomic fragment (cloned as plasmid pEPA) from Shewanella sp. strainSCRC2738 led to the identification of five open reading frames (Orfs),totaling 20 Kb, that are necessary and sufficient for EPA production inE. coli (Yazawa, (1996), supra). Several of the predicted proteindomains were homologues of FAS enzymes, while other regions showed nohomology to proteins of known function. At least 11 regions within thefive Orfs were identifiable as putative enzyme domains (See Metz et al.,Science 293:290-293 (2001)). When compared with sequences in the genedatabases, seven of these were more strongly related to PKS proteinsthan to FAS proteins. Included in this group were domains putativelyencoding malonyl-CoA:ACP acyltransferase (MAT), β-ketoacyl-ACP synthase(KS), β-ketoacyl-ACP reductase (KR), acyltransferase (AT),phosphopantetheine transferase, chain length (or chain initiation)factor (CLF) and a highly unusual cluster of six ACP domains (i.e., thepresence of more than two clustered ACP domains had not previously beenreported in PKS or FAS sequences). It is likely that the PKS pathway forPUFA synthesis that has been identified in Shewanella is widespread inmarine bacteria. Genes with high homology to the Shewanella gene clusterhave been identified in Photobacterium profundum (Allen et al., Appli.Environ. Microbiol. 65:1710 (1999)) and in Moritella marina (Vibriomarinus) (see U.S. Pat. No. 6,140,486, ibid., and Tanaka et al.,Biotechnol. Lett. 21:939 (1999)).

Polyunsaturated fatty acids (PUFAs) are considered to be useful fornutritional, pharmaceutical, industrial, and other purposes. Anexpansive supply of PUFAs from natural sources and from chemicalsynthesis are not sufficient for commercial needs. A major currentsource for PUFAs is from marine fish; however, fish stocks aredeclining, and this may not be a sustainable resource. Additionally,contamination, both heavy metal and toxic organic molecules, is aserious issue with oil derived from marine fish. Vegetable oils derivedfrom oil seed crops are relatively inexpensive and do not have thecontamination issues associated with fish oils. However, the PUFAs foundin commercially developed plant oils are typically limited to linoleicacid (eighteen carbons with 2 double bonds, in the delta 9 and 12positions—18:2 delta 9, 12) and linolenic acid (18:3 delta 9, 12, 15).In the conventional pathway for PUFA synthesis, medium chain-lengthsaturated fatty acids (products of a fatty acid synthase (FAS) system)are modified by a series of elongation and desaturation reactions.Because a number of separate desaturase and elongase enzymes arerequired for fatty acid synthesis from linoleic and linolenic acids toproduce the more saturated and longer chain PUFAs, engineering planthost cells for the expression of PUFAs such as EPA and docosahexaenoicacid (DHA) may require expression of several separate enzymes to achievesynthesis. Additionally, for production of useable quantities of suchPUFAs, additional engineering efforts may be required, for example,engineering the down regulation of enzymes that compete for substrate,engineering of higher enzyme activities such as by mutagenesis ortargeting of enzymes to plastid organelles. Therefore it is of interestto obtain genetic material involved in PUFA biosynthesis from speciesthat naturally produce these fatty acids and to express the isolatedmaterial alone or in combination in a heterologous system which can bemanipulated to allow production of commercial quantities of PUFAs.

The discovery of a PUFA PKS system in marine bacteria such as Shewanellaand Vibrio marinus (see U.S. Pat. No. 6,140,486, ibid.) provides aresource for new methods of commercial PUFA production. However, thesemarine bacteria have limitations which may ultimately restrict theirusefulness on a commercial level. First, although U.S. Pat. No.6,140,486 discloses that these marine bacteria PUFA PKS systems can beused to genetically modify plants, the marine bacteria naturally liveand grow in cold marine environments and the enzyme systems of thesebacteria do not function well above 22° C. In contrast, many cropplants, which are attractive targets for genetic manipulation using thePUFA PKS system, have normal growth conditions at temperatures above 22°C. and ranging to higher than 40° C. Therefore, the PUFA PKS systemsfrom these marine bacteria are not predicted to be readily adaptable toplant expression under normal growth conditions. Additionally, the knownmarine bacteria PUFA PKS systems do not directly produce triacylglyerols(TAG), whereas direct production of TAG would be desirable because TAGare a lipid storage product, and as a result, can be accumulated at veryhigh levels in cells, as opposed to a “structural” lipid product (e.g.phospholipids), which can generally only accumulate at low levels.

With regard to the production of eicosapentaenoic acid (EPA) inparticular, researchers have tried to produce EPA with microbes bygrowing them in both photosynthetic and heterotrophic cultures. Theyhave also used both classical and directed genetic approaches inattempts to increase the productively of the organisms under cultureconditions. Other researchers have attempted to produce EPA in oil-seedcrop plants by introduction of genes encoding various desaturase andelongase enzymes.

Researchers have attempted to use cultures of red microalgae (Monodus),diatoms (e.g. Phaeodactylum), other microalgae and fungi (e.g.Mortierella cultivated at low temperatures). However, in all cases,productivity was low compared to existing commercial microbialproduction systems for other long chain PUFAs such as DHA. In manycases, the EPA occurred primarily in the phospholipids (PL) rather thanthe triacylglycerols (TAG). Since productivity of microalgae underheterotrophic growth conditions can be much higher than underphototrophic conditions, researchers have attempted, and achieved,trophic conversion by introduction of genes encoding specific sugartransporters. However, even with the newly acquired heterotrophiccapability, productivity in terms of oil remained relatively low.

Efforts to produce EPA in oil-seed crop plants by modification of theendogenous fatty acid biosynthesis pathway have only yielded plants withvery low levels of the PUFA in their oils. As discussed above, severalmarine bacteria have been shown to produce PUFAs (EPA as well as DHA).However, these bacteria do not produce TAG and the EPA is foundprimarily in the PL membranes. The levels of EPA produced as well as thegrowth characteristics of these particular marine bacteria (discussedabove) limit their utility for commercial production of EPA.

Therefore, there is a need in the art for other PUFA PKS systems havinggreater flexibility for commercial use, and for a biological system thatefficiently produces quantities of lipids (PL and TAG) enriched indesired PUFAs, such as EPA, in a commercially useful production process.

SUMMARY OF THE INVENTION

One embodiment of the present invention relates to an isolated nucleicacid molecule. The nucleic acid molecule comprises a nucleic acidsequence selected from: (a) a nucleic acid sequence encoding an aminoacid sequence selected from the group consisting of: SEQ ID NO:39, SEQID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:48, SEQ ID NO:50, SEQ IDNO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ IDNO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68 and biologically activefragments thereof; (b) a nucleic acid sequence encoding an amino acidsequence that is at least about 60% identical, and more preferably atleast about 70% identical, and more preferably at least about 80%identical, and more preferably at least about 90% identical, to an aminoacid sequence selected from the group consisting of: SEQ ID NO:39, SEQID NO:43, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:56 and SEQ ID NO:58,wherein the amino acid sequence has a biological activity of at leastone domain of a polyunsaturated fatty acid (PUFA) polyketide synthase(PKS) system; (c) a nucleic acid sequence encoding an amino acidsequence that is at least about 65% identical, and more preferably atleast about 70% identical, and more preferably at least about 80%identical, and more preferably at least about 90% identical, to SEQ IDNO:54, wherein the amino acid sequence has a biological activity of atleast one domain of a polyunsaturated fatty acid (PUFA) polyketidesynthase (PKS) system; (d) a nucleic acid sequence encoding an aminoacid sequence that is at least about 70% identical, and more preferablyat least about 80% identical, and more preferably at least about 90%identical, to an amino acid sequence selected from the group consistingof: SEQ ID NO:45, SEQ ID NO:48, SEQ ID NO:60, SEQ ID NO:62 and SEQ IDNO:64, wherein the amino acid sequence has a biological activity of atleast one domain of a polyunsaturated fatty acid (PUFA) polyketidesynthase (PKS) system; (e) a nucleic acid sequence encoding an aminoacid sequence that is at least about 80% identical, and more preferablyat least about 90% identical, to an amino acid sequence selected fromthe group consisting of: SEQ ID NO:41, SEQ ID NO:66, SEQ ID NO:68,wherein the amino acid sequence has a biological activity of at leastone domain of a polyunsaturated fatty acid (PUFA) polyketide synthase(PKS) system; and/or (f) a nucleic acid sequence that is fullycomplementary to the nucleic acid sequence of (a), (b), (c), (d), or(e). In one aspect, the nucleic acid sequence encodes an amino acidsequence selected from: SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ IDNO:45, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ IDNO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ IDNO:66, SEQ ID NO:68, and biologically active fragments thereof. In oneaspect, the nucleic acid sequence is selected from the group consistingof: SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ IDNO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ IDNO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, and SEQID NO:67.

Another embodiment of the present invention relates to a recombinantnucleic acid molecule comprising any of the above-described nucleic acidmolecules, operatively linked to at least one transcription controlsequence.

Yet another embodiment of the present invention relates to a recombinantcell transfected with any of the above-described recombinant nucleicacid molecules. Another embodiment of the present invention relates to agenetically modified microorganism, wherein the microorganism expressesa PKS system comprising at least one biologically active domain of apolyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system,wherein the at least one domain of the PUFA PKS system comprises anamino acid sequence selected from: (a) an amino acid sequence selectedfrom the group consisting of: SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43,SEQ ID NO:45, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54,SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64,SEQ ID NO:66, SEQ ID NO:68 and biologically active fragments thereof;(b) an amino acid sequence that is at least about 60% identical, andmore preferably at least about 70% identical, and more preferably atleast about 80% identical, and more preferably at least about 90%identical, to an amino acid sequence selected from the group consistingof: SEQ ID NO:39, SEQ ID NO:43, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:56and SEQ ID NO:58, wherein the amino acid sequence has a biologicalactivity of at least one domain of a polyunsaturated fatty acid (PUFA)polyketide synthase (PKS) system; (c) an amino acid sequence that is atleast about 65% identical, and more preferably at least about 70%identical, and more preferably at least about 80% identical, and morepreferably at least about 90% identical, to SEQ ID NO:54, wherein theamino acid sequence has a biological activity of at least one domain ofa polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system;(d) an amino acid sequence that is at least about 70% identical, andmore preferably at least about 80% identical, and more preferably atleast about 90% identical, to an amino acid sequence selected from thegroup consisting of: SEQ ID NO:45, SEQ ID NO:48, SEQ ID NO:60, SEQ IDNO:62 and SEQ ID NO:64, wherein the amino acid sequence has a biologicalactivity of at least one domain of a polyunsaturated fatty acid (PUFA)polyketide synthase (PKS) system; and/or (e) an amino acid sequence thatis at least about 80% identical, and more preferably at least about 90%identical, to an amino acid sequence selected from the group consistingof: SEQ ID NO:41, SEQ ID NO:66, SEQ ID NO:68, wherein the amino acidsequence has a biological activity of at least one domain of apolyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system. Themicroorganism is genetically modified to affect the activity of the PKSsystem.

In one aspect, the microorganism is genetically modified by transfectionwith a recombinant nucleic acid molecule encoding the at least onedomain of a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS)system. For example, the microorganism can include a Thraustochytrid,such as a Schizochytrium. In one aspect, such a microorganism has beenfurther genetically modified to recombinantly express at least onenucleic acid molecule encoding at least one biologically active domainfrom a PKS system selected from the group consisting of: a bacterialPUFA PKS system, a Type I PKS system, a Type II PKS system, a modularPKS system, and a non-bacterial PUFA PKS system. The non-bacterial PUFAPKS system can include a Thraustochytrid PUFA PKS system and in oneaspect, a Schizochytrium PUFA PKS system.

In another aspect, the microorganism endogenously expresses a PKS systemcomprising the at least one domain of the PUFA PKS system, and whereinthe genetic modification is in a nucleic acid sequence encoding at leastone domain of the PUFA PKS system. In another aspect, such amicroorganism has been further genetically modified to recombinantlyexpress at least one nucleic acid molecule encoding at least onebiologically active domain from a PKS system selected from the groupconsisting of: a bacterial PUFA PKS system, a Type I PKS system, a TypeII PKS system, a modular PKS system, and a non-bacterial PUFA PKS system(e.g., a Thraustochytrid PUFA PKS system, such as a Schizochytrium PUFAPKS system).

In another aspect, the microorganism endogenously expresses a PUFA PKSsystem comprising the at least one biologically active domain of a PUFAPKS system, and wherein the genetic modification comprises expression ofa recombinant nucleic acid molecule selected from the group consistingof a recombinant nucleic acid molecule encoding at least onebiologically active domain from a second PKS system and a recombinantnucleic acid molecule encoding a protein that affects the activity ofthe endogenous PUFA PKS system. The biologically active domain from asecond PKS system can include, but is not limited to: (a) a domain of apolyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system froma Thraustochytrid microorganism; (b) a domain of a PUFA PKS system froma microorganism identified by the following method: (i) selecting amicroorganism that produces at least one PUFA; and, (ii) identifying amicroorganism from (i) that has an ability to produce increased PUFAsunder dissolved oxygen conditions of less than about 5% of saturation inthe fermentation medium, as compared to production of PUFAs by themicroorganism under dissolved oxygen conditions of greater than about 5%of saturation in the fermentation medium; (c) a domain comprising anamino acid sequence selected from the group consisting of: SEQ ID NO:2,SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:13, SEQID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ IDNO:28, SEQ ID NO:30, SEQ ID NO:32, and biologically active fragmentsthereof; and (d) a domain comprising an amino acid sequence that is atleast about 60% identical, and more preferably at least about 70%identical, and more preferably at least about 80% identical, and morepreferably at least about 90% identical, to the amino acid sequence of(c), wherein the amino acid sequence has a biological activity of atleast one domain of a polyunsaturated fatty acid (PUFA) polyketidesynthase (PKS) system. In one aspect, recombinant nucleic acid moleculeencodes a phosphopantetheine transferase. In one aspect, the second PKSsystem is selected from the group consisting of: a bacterial PUFA PKSsystem, a type I PKS system, a type II PKS system, a modular PKS system,and a non-bacterial PUFA PKS system (e.g., a eukaryotic PUFA PKS system,such as a Thraustochytrid PUFA PKS system, including, but not limited toa Schizochytrium PUFA PKS system).

Yet another embodiment of the present invention relates to a geneticallymodified plant, wherein the plant has been genetically modified torecombinantly express a PKS system comprising at least one biologicallyactive domain of a polyunsaturated fatty acid (PUFA) polyketide synthase(PKS) system, wherein the domain comprises an amino acid sequenceselected from the group consisting of: (a) an amino acid sequenceselected from the group consisting of: SEQ ID NO:39, SEQ ID NO:41, SEQID NO:43, SEQ ID NO:45, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ IDNO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ IDNO:64, SEQ ID NO:66, SEQ ID NO:68 and biologically active fragmentsthereof; (b) an amino acid sequence that is at least about 60%identical, and more preferably at least about 70% identical, and morepreferably at least about 80% identical, and more preferably at leastabout 90% identical, to an amino acid sequence selected from the groupconsisting of: SEQ ID NO:39, SEQ ID NO:43, SEQ ID NO:50, SEQ ID NO:52,SEQ ID NO:56 and SEQ ID NO:58, wherein the amino acid sequence has abiological activity of at least one domain of a polyunsaturated fattyacid (PUFA) polyketide synthase (PKS) system; (c) an amino acid sequencethat is at least about 65% identical, and more preferably at least about70% identical, and more preferably at least about 80% identical, andmore preferably at least about 90% identical, to SEQ ID NO:54, whereinthe amino acid sequence has a biological activity of at least one domainof a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system;(d) an amino acid sequence that is at least about 70% identical, andmore preferably at least about 80% identical, and more preferably atleast about 90% identical, to an amino acid sequence selected from thegroup consisting of: SEQ ID NO:45, SEQ ID NO:48, SEQ ID NO:60, SEQ IDNO:62 and SEQ ID NO:64, wherein the amino acid sequence has a biologicalactivity of at least one domain of a polyunsaturated fatty acid (PUFA)polyketide synthase (PKS) system; and/or (e) an amino acid sequence thatis at least about 80% identical, and more preferably at least about 90%identical, to an amino acid sequence selected from the group consistingof: SEQ ID NO:41, SEQ ID NO:66, SEQ ID NO:68, wherein the amino acidsequence has a biological activity of at least one domain of apolyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system. Inone aspect, the at least one domain of the PUFA PKS system comprises anamino acid sequence selected from the group consisting of: SEQ ID NO:39,SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:48, SEQ ID NO:50,SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60,SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66 and SEQ ID NO:68 andbiologically active fragments thereof. In one aspect, the plant has beenfurther genetically modified to recombinantly express at least onenucleic acid molecule encoding at least one biologically active domainfrom a PKS system selected from the group consisting of: a bacterialPUFA PKS system, a Type I PKS system, a Type II PKS system, a modularPKS system, and a non-bacterial PUFA PKS system (e.g., a ThraustochytridPUFA PKS system, such as a Schizochytrium PUFA PKS system).

Yet another embodiment of the present invention relates to a method toproduce a bioactive molecule that is produced by a polyketide synthasesystem, comprising culturing under conditions effective to produce thebioactive molecule a genetically modified organism that expresses a PKSsystem comprising at least one biologically active domain of apolyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system,wherein the at least one domain of the PUFA PKS system comprises anamino acid sequence selected from the group consisting of: (a) an aminoacid sequence selected from the group consisting of: SEQ ID NO:39, SEQID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:48, SEQ ID NO:50, SEQ IDNO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ IDNO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68 and biologically activefragments thereof; (b) an amino acid sequence that is at least about 60%identical, and more preferably at least about 70% identical, and morepreferably at least about 80% identical, and more preferably at leastabout 90% identical, to an amino acid sequence selected from the groupconsisting of: SEQ ID NO:39, SEQ ID NO:43, SEQ ID NO:50, SEQ ID NO:52,SEQ ID NO:56 and SEQ ID NO:58, wherein the amino acid sequence has abiological activity of at least one domain of a polyunsaturated fattyacid (PUFA) polyketide synthase (PKS) system; (c) an amino acid sequencethat is at least about 65% identical, and more preferably at least about70% identical, and more preferably at least about 80% identical, andmore preferably at least about 90% identical, to SEQ ID NO:54, whereinthe amino acid sequence has a biological activity of at least one domainof a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system;(d) an amino acid sequence that is at least about 70% identical, andmore preferably at least about 80% identical, and more preferably atleast about 90% identical, to an amino acid sequence selected from thegroup consisting of: SEQ ID NO:45, SEQ ID NO:48, SEQ ID NO:60, SEQ IDNO:62 and SEQ ID NO:64, wherein the amino acid sequence has a biologicalactivity of at least one domain of a polyunsaturated fatty acid (PUFA)polyketide synthase (PKS) system; and/or (e) an amino acid sequence thatis at least about 80% identical, and more preferably at least about 90%identical, to an amino acid sequence selected from the group consistingof: SEQ ID NO:41, SEQ ID NO:66, SEQ ID NO:68, wherein the amino acidsequence has a biological activity of at least one domain of apolyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system.

In one aspect, the organism endogenously expresses a PKS systemcomprising the at least one domain of the PUFA PKS system, and whereinthe genetic modification is in a nucleic acid sequence encoding the atleast one domain of the PUFA PKS system. In one aspect, the geneticmodification changes at least one product produced by the endogenous PKSsystem, as compared to an organism wherein the PUFA PKS system has notbeen genetically modified.

In another aspect, the organism endogenously expresses a PKS systemcomprising the at least one biologically active domain of the PUFA PKSsystem, and the genetic modification comprises transfection of theorganism with a recombinant nucleic acid molecule selected from thegroup consisting of: a recombinant nucleic acid molecule encoding atleast one biologically active domain from a second PKS system and arecombinant nucleic acid molecule encoding a protein that affects theactivity of the PUFA PKS system. In one aspect, the genetic modificationchanges at least one product produced by the endogenous PKS system, ascompared to an organism that has not been genetically modified to affectPUFA production.

In another aspect, the organism is genetically modified by transfectionwith a recombinant nucleic acid molecule encoding the at least onedomain of the polyunsaturated fatty acid (PUFA) polyketide synthase(PKS) system.

In another aspect, the organism produces a polyunsaturated fatty acid(PUFA) profile that differs from the naturally occurring organismwithout a genetic modification.

In another aspect, the organism endogenously expresses a non-bacterialPUFA PKS system, and wherein the genetic modification comprisessubstitution of a domain from a different PKS system for a nucleic acidsequence encoding at least one domain of the non-bacterial PUFA PKSsystem.

In yet another aspect, the organism endogenously expresses anon-bacterial PUFA PKS system that has been modified by transfecting theorganism with a recombinant nucleic acid molecule encoding a proteinthat regulates the chain length of fatty acids produced by the PUFA PKSsystem.

In another aspect, the bioactive molecule is selected from: ananti-inflammatory formulation, a chemotherapeutic agent, an activeexcipient, an osteoporosis drug, an anti-depressant, an anti-convulsant,an anti-Heliobactor pylori drug, a drug for treatment ofneurodegenerative disease, a drug for treatment of degenerative liverdisease, an antibiotic, and/or a cholesterol lowering formulation. Inone aspect, the bioactive molecule is an antibiotic. In another aspect,the bioactive molecule is a polyunsaturated fatty acid (PUFA). In yetanother aspect, the bioactive molecule is a molecule includingcarbon-carbon double bonds in the cis configuration. In one aspect, thebioactive molecule is a molecule including a double bond at every thirdcarbon. In one aspect, the organism is a microorganism. In anotheraspect, the organism is a plant.

Another embodiment of the present invention relates to a method toproduce a plant that has a polyunsaturated fatty acid (PUFA) profilethat differs from the naturally occurring plant, comprising geneticallymodifying cells of the plant to express a PKS system comprising at leastone recombinant nucleic acid molecule comprising a nucleic acid sequenceencoding at least one biologically active domain of a PUFA PKS system,wherein the at least one domain of the PUFA PKS system comprises anamino acid sequence selected from the group consisting of: (a) an aminoacid sequence selected from the group consisting of: SEQ ID NO:39, SEQID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:48, SEQ ID NO:50, SEQ IDNO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ IDNO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68 and biologically activefragments thereof; (b) an amino acid sequence that is at least about 60%identical, and more preferably at least about 70% identical, and morepreferably at least about 80% identical, and more preferably at leastabout 90% identical, to an amino acid sequence selected from the groupconsisting of: SEQ ID NO:39, SEQ ID NO:43, SEQ ID NO:50, SEQ ID NO:52,SEQ ID NO:56 and SEQ ID NO:58, wherein the amino acid sequence has abiological activity of at least one domain of a polyunsaturated fattyacid (PUFA) polyketide synthase (PKS) system; (c) an amino acid sequencethat is at least about 65% identical, and more preferably at least about70% identical, and more preferably at least about 80% identical, andmore preferably at least about 90% identical, to SEQ ID NO:54, whereinthe amino acid sequence has a biological activity of at least one domainof a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system;(d) an amino acid sequence that is at least about 70% identical, andmore preferably at least about 80% identical, and more preferably atleast about 90% identical, to an amino acid sequence selected from thegroup consisting of: SEQ ID NO:45, SEQ ID NO:48, SEQ ID NO:60, SEQ IDNO:62 and SEQ ID NO:64, wherein the amino acid sequence has a biologicalactivity of at least one domain of a polyunsaturated fatty acid (PUFA)polyketide synthase (PKS) system; and (e) an amino acid sequence that isat least about 80% identical, and more preferably at least about 90%identical, to an amino acid sequence selected from the group consistingof: SEQ ID NO:41, SEQ ID NO:66, SEQ ID NO:68, wherein the amino acidsequence has a biological activity of at least one domain of apolyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system.

Another embodiment of the present invention relates to a method tomodify an endproduct containing at least one fatty acid, comprisingadding to the endproduct an oil produced by a recombinant host cell thatexpresses at least one recombinant nucleic acid molecule comprising anucleic acid sequence encoding at least one biologically active domainof a PUFA PKS system, wherein the at least one domain of a PUFA PKSsystem comprises an amino acid sequence selected from the groupconsisting of: (a) an amino acid sequence selected from the groupconsisting of: SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45,SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56,SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66,SEQ ID NO:68 and biologically active fragments thereof; (b) an aminoacid sequence that is at least about 60% identical, and more preferablyat least about 70% identical, and more preferably at least about 80%identical, and more preferably at least about 90% identical, to an aminoacid sequence selected from the group consisting of: SEQ ID NO:39, SEQID NO:43, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:56 and SEQ ID NO:58,wherein the amino acid sequence has a biological activity of at leastone domain of a polyunsaturated fatty acid (PUFA) polyketide synthase(PKS) system; (c) an amino acid sequence that is at least about 65%identical, and more preferably at least about 70% identical, and morepreferably at least about 80% identical, and more preferably at leastabout 90% identical, to SEQ ID NO:54, wherein the amino acid sequencehas a biological activity of at least one domain of a polyunsaturatedfatty acid (PUFA) polyketide synthase (PKS) system; (d) an amino acidsequence that is at least about 70% identical, and more preferably atleast about 80% identical, and more preferably at least about 90%identical, to an amino acid sequence selected from the group consistingof: SEQ ID NO:45, SEQ ID NO:48, SEQ ID NO:60, SEQ ID NO:62 and SEQ IDNO:64, wherein the amino acid sequence has a biological activity of atleast one domain of a polyunsaturated fatty acid (PUFA) polyketidesynthase (PKS) system; and (e) an amino acid sequence that is at leastabout 80% identical, and more preferably at least about 90% identical,to an amino acid sequence selected from the group consisting of: SEQ IDNO:41, SEQ ID NO:66, SEQ ID NO:68, wherein the amino acid sequence has abiological activity of at least one domain of a polyunsaturated fattyacid (PUFA) polyketide synthase (PKS) system. In one aspect, theendproduct is selected from: a dietary supplement, a food product, apharmaceutical formulation, a humanized animal milk, and an infantformula. In one aspect, the pharmaceutical formulation is selected fromthe group consisting of an anti-inflammatory formulation, achemotherapeutic agent, an active excipient, an osteoporosis drug, ananti-depressant, an anti-convulsant, an anti-Heliobactor pylon drug, adrug for treatment of neurodegenerative disease, a drug for treatment ofdegenerative liver disease, an antibiotic, and a cholesterol loweringformulation. In one aspect, the endproduct is used to treat a conditionselected from the group consisting of: chronic inflammation, acuteinflammation, gastrointestinal disorder, cancer, cachexia, cardiacrestenosis, neurodegenerative disorder, degenerative disorder of theliver, blood lipid disorder, osteoporosis, osteoarthritis, autoimmunedisease, preeclampsia, preterm birth, age related maculopathy, pulmonarydisorder, and peroxisomal disorder.

Yet another embodiment of the present invention relates to a method toproduce a humanized animal milk, comprising genetically modifyingmilk-producing cells of a milk-producing animal with at least onerecombinant nucleic acid molecule comprising a nucleic acid sequenceencoding at least one biologically active domain of a PUFA PKS system,wherein the at least one domain of the PUFA PKS system comprises anamino acid sequence selected from the group consisting of: (a) an aminoacid sequence selected from the group consisting of: SEQ ID NO:39, SEQID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:48, SEQ ID NO:50, SEQ IDNO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ IDNO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68 and biologically activefragments thereof; (b) an amino acid sequence that is at least about 60%identical, and more preferably at least about 70% identical, and morepreferably at least about 80% identical, and more preferably at leastabout 90% identical, to an amino acid sequence selected from the groupconsisting of: SEQ ID NO:39, SEQ ID NO:43, SEQ ID NO:50, SEQ ID NO:52,SEQ ID NO:56 and SEQ ID NO:58, wherein the amino acid sequence has abiological activity of at least one domain of a polyunsaturated fattyacid (PUFA) polyketide synthase (PKS) system; (c) an amino acid sequencethat is at least about 65% identical, and more preferably at least about70% identical, and more preferably at least about 80% identical, andmore preferably at least about 90% identical, to SEQ ID NO:54, whereinthe amino acid sequence has a biological activity of at least one domainof a polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system;(d) an amino acid sequence that is at least about 70% identical, andmore preferably at least about 80% identical, and more preferably atleast about 90% identical, to an amino acid sequence selected from thegroup consisting of: SEQ ID NO:45, SEQ ID NO:48, SEQ ID NO:60, SEQ IDNO:62 and SEQ ID NO:64, wherein the amino acid sequence has a biologicalactivity of at least one domain of a polyunsaturated fatty acid (PUFA)polyketide synthase (PKS) system; and (e) an amino acid sequence that isat least about 80% identical, and more preferably at least about 90%identical, to an amino acid sequence selected from the group consistingof: SEQ ID NO:41, SEQ ID NO:66, SEQ ID NO:68, wherein the amino acidsequence has a biological activity of at least one domain of apolyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system.

Another embodiment of the present invention relates to a geneticallymodified Thraustochytrid microorganism, wherein the microorganism has anendogenous polyunsaturated fatty acid (PUFA) polyketide synthase (PKS)system, and wherein the endogenous PUFA PKS system has been geneticallymodified to alter the expression profile of a polyunsaturated fatty acid(PUFA) by the Thraustochytrid microorganism as compared to theThraustochytrid microorganism in the absence of the geneticmodification.

In one aspect, the endogenous PUFA PKS system has been modified bymutagenesis of a nucleic acid sequence that encodes at least one domainof the endogenous PUFA PKS system. In one aspect, the modification isproduced by targeted mutagenesis. In another aspect, the modification isproduced by classical mutagenesis and screening.

In another aspect, the endogenous PUFA PKS system has been modified bydeleting at least one nucleic acid sequence that encodes at least onedomain of the endogenous PUFA PKS system and inserting therefore anucleic acid sequence encoding a homologue of the endogenous domain toalter the PUFA production profile of the Thraustochytrid microorganism,wherein the homologue has a biological activity of at least one domainof a PKS system. In one aspect, the homologue of the endogenous domaincomprises a modification, as compared to the endogenous domain, selectedfrom the group consisting of at least one deletion, insertion orsubstitution that results in an alteration of PUFA production profile bythe microorganism. In another aspect, the amino acid sequence of thehomologue is at least about 60% identical, and more preferably about 70%identical, and more preferably about 80% identical, and more preferablyabout 90% identical to the amino acid sequence of the endogenous domain.In one aspect, homologue of the endogenous domain is a domain from aPUFA PKS system of another Thraustochytrid microorganism.

In another aspect, the endogenous PUFA PKS system has been modified bydeleting at least one nucleic acid sequence that encodes at least onedomain of the endogenous PUFA PKS system and inserting therefore anucleic acid sequence encoding at least one domain of a PKS system froma different microorganism. In one aspect, the nucleic acid sequenceencoding at least one domain of a PKS system from a differentmicroorganism is from a bacterial PUFA PKS system. For example, thedifferent microorganism can be a marine bacteria having a PUFA PKSsystem that naturally produces PUFAs at a temperature of about 25° C. orgreater. In one aspect, the marine bacteria is selected from the groupconsisting of Shewanella olleyana and Shewanella japonica. In oneaspect, the domain of a PKS system from a different microorganism isfrom a PKS system selected from the group consisting of: a Type I PKSsystem, a Type II PKS system, a modular PKS system, and a PUFA PKSsystem from a different Thraustochytrid microorganism.

In any of the above aspects, the domain of the endogenous PUFA PKSsystem can include, but is not limited to, a domain having a biologicalactivity of at least one of the following proteins: malonyl-CoA:ACPacyltransferase (MAT), β-keto acyl-ACP synthase (KS), ketoreductase(KR), acyltransferase (AT), FabA-like β-hydroxy acyl-ACP dehydrase (DH),phosphopantetheine transferase, chain length factor (CLF), acyl carrierprotein (ACP), enoyl ACP-reductase (ER), an enzyme that catalyzes thesynthesis of trans-2-acyl-ACP, an enzyme that catalyzes the reversibleisomerization of trans-2-acyl-ACP to cis-3-acyl-ACP, and an enzyme thatcatalyzes the elongation of cis-3-acyl-ACP to cis-5-β-keto-acyl-ACP. Inany of the above aspects, the domain of the endogenous PUFA PKS systemcan include an amino acid sequence selected from the group consistingof: (a) an amino acid sequence selected from the group consisting of:SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ IDNO:13, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ IDNO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:39, SEQ IDNO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:48, SEQ ID NO:50, SEQ IDNO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ IDNO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68 and biologically activefragments thereof; and (b) an amino acid sequence that is at least about60% identical, and more preferably at least about 70% identical, andmore preferably at least about 80% identical, and more preferably atleast about 90% identical, to an amino acid sequence of (a), wherein theamino acid sequence has a biological activity of at least one domain ofa polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system.

In one aspect, the PUFA production profile is altered to initiate,increase or decrease production of eicosapentaenoic acid (EPA) by themicroorganism. In another aspect, the PUFA production profile is alteredto initiate, increase or decrease production of docosahexaenoic acid(DHA) by the microorganism. In another aspect, the PUFA productionprofile is altered to initiate, increase or decrease production of oneor both isomers of docosapentaenoic acid (DPA) by the microorganism. Inanother aspect, the PUFA production profile is altered to initiate,increase or decrease production of arachidonic acid (ARA) by themicroorganism. In another aspect, the Thraustochytrid is from a genusselected from the group consisting of Schizochytrium, Thraustochytrium,and Japonochytrium. In another aspect, the Thraustochytrid is from thegenus Schizochytrium. In another aspect, the Thraustochytrid is from aSchizochytrium species selected from the group consisting of:Schizochytrium aggregatum, Schizochytrium limacinum, and Schizochytriumminutum. In another aspect, the Thraustochytrid is from the genusThraustochytrium.

Yet another embodiment of the present invention relates to a geneticallymodified Schizochytrium that produces eicosapentaenoic acid (EPA),wherein the Schizochytrium has an endogenous polyunsaturated fatty acid(PUFA) polyketide synthase (PKS) system comprising a geneticmodification in at least one nucleic acid sequence that encodes at leastone domain of the endogenous PUFA PKS system that results in theproduction of EPA by the Schizochytrium. In one aspect, theSchizochytrium comprises a genetic modification in at least one nucleicacid sequence encoding at least one domain having a biological activityof at least one of the following proteins: malonyl-CoA:ACPacyltransferase (MAT), β-keto acyl-ACP synthase (KS), ketoreductase(KR), acyltransferase (AT), FabA-like β-hydroxy acyl-ACP dehydrase (DH),phosphopantetheine transferase, chain length factor (CLF), acyl carrierprotein (ACP), enoyl ACP-reductase (ER), an enzyme that catalyzes thesynthesis of trans-2-acyl-ACP, an enzyme that catalyzes the reversibleisomerization of trans-2-acyl-ACP to cis-3-acyl-ACP, and an enzyme thatcatalyzes the elongation of cis-3-acyl-ACP to cis-5-β-keto-acyl-ACP. Inone aspect, the Schizochytrium comprises a genetic modification in atleast one nucleic acid sequence encoding at least one domain from theopen reading frame encoding SEQ ID NO:2 of the endogenous PUFA PKSsystem. In one aspect, the Schizochytrium comprises a geneticmodification in at least one nucleic acid sequence encoding at least onedomain from the open reading frame encoding SEQ ID NO:4 of theendogenous PUFA PKS system. In one aspect, the Schizochytrium comprisesa genetic modification in at least one nucleic acid sequence encoding atleast one domain from the open reading frame encoding SEQ ID NO:6 of theendogenous PUFA PKS system. In one aspect, the Schizochytrium comprisesa genetic modification in at least one nucleic acid sequence encoding atleast one domain having a biological activity of at least one of thefollowing proteins: β-keto acyl-ACP synthase (KS), FabA-like β-hydroxyacyl-ACP dehydrase (DH), chain length factor (CLF), an enzyme thatcatalyzes the synthesis of trans-2-acyl-ACP, an enzyme that catalyzesthe reversible isomerization of trans-2-acyl-ACP to cis-3-acyl-ACP, andan enzyme that catalyzes the elongation of cis-3-acyl-ACP tocis-5-β-keto-acyl-ACP. In one aspect, the Schizochytrium comprises agenetic modification in at least one nucleic acid sequence encoding anamino acid sequence selected from the group consisting of SEQ ID NO:20,SEQ ID NO:22, SEQ ID NO:28 and SEQ ID NO:30 of the endogenous PUFA PKSsystem. In one aspect, the Schizochytrium has been modified by deletingat least one nucleic acid sequence that encodes at least one domain ofthe endogenous PUFA PKS system and inserting therefore a nucleic acidsequence encoding at least one domain of a PKS system from anon-Schizochytrium microorganism. In one aspect, the non-Schizochytriummicroorganism grows and produces PUFAs at temperature of at least about15° C., and more preferably at least about 20° C., and more preferablyat least about 25° C., and more preferably at least about 30° C., andmore preferably between about 20° C. and about 40° C. In one aspect, thenucleic acid sequence encoding at least one domain of a PKS system froma non-Schizochytrium microorganism is from a bacterial PUFA PKS system.In one aspect, the bacterial PUFA PKS system is from a bacteriumselected from the group consisting of Shewanella olleyana and Shewanellajaponica. In another aspect, the nucleic acid sequence encoding at leastone domain of a PKS system is selected from the group consisting of aType I PKS system, a Type II PKS system, a modular PKS system, and anon-bacterial PUFA PKS system (e.g., a eukaryotic PUFA PKS system, suchas a Thraustochytrid PUFA PKS system).

Another embodiment of the present invention relates to a geneticallymodified Schizochytrium that produces increased amounts ofdocosahexaenoic acid (DHA) as compared to a non-genetically modifiedSchizochytrium, wherein the Schizochytrium has an endogenouspolyunsaturated fatty acid (PUFA) polyketide synthase (PKS) systemcomprising a genetic modification in at least one nucleic sequence thatencodes at least one domain of the endogenous PUFA PKS system thatresults in increased the production of DHA by the Schizochytrium. In oneaspect, at least one domain of the endogenous PUFA PKS system has beenmodified by substitution for at least one domain of a PUFA PKS systemfrom Thraustochytrium. In one aspect, the ratio of DHA to DPA producedby the Schizochytrium is increased as compared to a non-geneticallymodified Schizochytrium.

Another embodiment of the present invention relates to a method toproduce lipids enriched for at least one selected polyunsaturated fattyacid (PUFA), comprising culturing under conditions effective to producethe lipids a genetically modified Thraustochytrid microorganism asdescribed above or a genetically modified Schizochytrium as describedabove. In one aspect, the selected PUFA is eicosapentaenoic acid (EPA).

Yet another embodiment of the present invention relates to a method toproduce eicosapentaenoic acid (EPA)-enriched lipids, comprisingculturing under conditions effective to produce the EPA-enriched lipidsa genetically modified Thraustochytrid microorganism, wherein themicroorganism has an endogenous polyunsaturated fatty acid (PUFA)polyketide synthase (PKS) system, and wherein the endogenous PUFA PKSsystem has been genetically modified in at least one domain to initiateor increase the production of EPA in the lipids of the microorganism ascompared to in the absence of the modification.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a graphical representation of the domain structure of theSchizochytrium PUFA PKS system.

FIG. 2 shows a comparison of domains of PUFA PKS systems fromSchizochytrium and Shewanella.

FIG. 3 shows a comparison of domains of PUFA PKS systems fromSchizochytrium and a related PKS system from Nostoc whose product is along chain fatty acid that does not contain any double bonds.

DETAILED DESCRIPTION OF THE INVENTION

The present invention generally relates to polyunsaturated fatty acid(PUFA) polyketide synthase (PKS) systems, to genetically modifiedorganisms comprising such PUFA PKS systems, to methods of making andusing such systems for the production of products of interest, includingbioactive molecules and particularly, PUFAs, such as DHA, DPA and EPA.As used herein, a PUFA PKS system generally has the followingidentifying features: (1) it produces PUFAs as a natural product of thesystem; and (2) it comprises several multifunctional proteins assembledinto a complex that conducts both iterative processing of the fatty acidchain as well non-iterative processing, including trans-cisisomerization and enoyl reduction reactions in selected cycles (See FIG.1, for example). Reference to a PUFA PKS system refers collectively toall of the genes and their encoded products that work in a complex toproduce PUFAs in an organism. Therefore, the PUFA PKS system refersspecifically to a PKS system for which the natural products are PUFAs.

More specifically, first, a PUFA PKS system that forms the basis of thisinvention produces polyunsaturated fatty acids (PUFAs) as products(i.e., an organism that endogenously (naturally) contains such a PKSsystem makes PUFAs using this system). The PUFAs referred to herein arepreferably polyunsaturated fatty acids with a carbon chain length of atleast 16 carbons, and more preferably at least 18 carbons, and morepreferably at least 20 carbons, and more preferably 22 or more carbons,with at least 3 or more double bonds, and preferably 4 or more, and morepreferably 5 or more, and even more preferably 6 or more double bonds,wherein all double bonds are in the cis configuration. It is an objectof the present invention to find or create via genetic manipulation ormanipulation of the endproduct, PKS systems which producepolyunsaturated fatty acids of desired chain length and with desirednumbers of double bonds. Examples of PUFAs include, but are not limitedto, DHA (docosahexaenoic acid (C22:6, ω-3)), ARA (eicosatetraenoic acidor arachidonic acid (C20:4, n-6)), DPA (docosapentaenoic acid (C22:5,ω-6 or ω-3)), and EPA (eicosapentaenoic acid (C20:5, ω-3)).

Second, the PUFA PKS system described herein incorporates both iterativeand non-iterative reactions, which distinguish the system frompreviously described PKS systems (e.g., type I, type II or modular).More particularly, the PUFA PKS system described herein contains domainsthat appear to function during each cycle as well as those which appearto function during only some of the cycles. A key aspect of thisfunctionality may be related to the domains showing homology to thebacterial Fab-A enzymes. For example, the Fab-A enzyme of E. coli hasbeen shown to possess two enzymatic activities. It possesses adehydration activity in which a water molecule (H₂O) is abstracted froma carbon chain containing a hydroxy group, leaving a trans double bondin that carbon chain. In addition, it has an isomerase activity in whichthe trans double bond is converted to the cis configuration. Thisisomerization is accomplished in conjunction with a migration of thedouble bond position to adjacent carbons. In PKS (and FAS) systems, themain carbon chain is extended in 2 carbon increments. One can thereforepredict the number of extension reactions required to produce the PUFAproducts of these PKS systems. For example, to produce DHA (C22:6, allcis) requires 10 extension reactions. Since there are only 6 doublebonds in the end product, it means that during some of the reactioncycles, a double bond is retained (as a cis isomer), and in others, thedouble bond is reduced prior to the next extension.

Before the discovery of a PUFA PKS system in marine bacteria (see U.S.Pat. No. 6,140,486), PKS systems were not known to possess thiscombination of iterative and selective enzymatic reactions, and theywere not thought of as being able to produce carbon-carbon double bondsin the cis configuration. However, the PUFA PKS system described by thepresent invention has the capacity to introduce cis double bonds and thecapacity to vary the reaction sequence in the cycle.

The present inventors propose to use these features of the PUFA PKSsystem to produce a range of bioactive molecules that could not beproduced by the previously described (Type II, Type I and modular) PKSsystems. These bioactive molecules include, but are not limited to,polyunsaturated fatty acids (PUFAs), antibiotics or other bioactivecompounds, many of which will be discussed below. For example, using theknowledge of the PUFA PKS gene structures described herein, any of anumber of methods can be used to alter the PUFA PKS genes, or combineportions of these genes with other synthesis systems, including otherPKS systems, such that new products are produced. The inherent abilityof this particular type of system to do both iterative and selectivereactions will enable this system to yield products that would not befound if similar methods were applied to other types of PKS systems.

Much of the structure of the PKS system for PUFA synthesis in theeukaryotic Thraustochytrid, Schizochytrium has been described in detailin U.S. Pat. No. 6,566,583. Complete sequencing of cDNA and genomicclones in Schizochytrium by the present inventors allowed theidentification of the full-length genomic sequence of each of OrfA, OrfBand OrfC and the complete identification of the specific domains inthese Schizochytrium Orfs with homology to those in Shewanella (see FIG.2 and U.S. patent application Ser. No. 10/124,800, supra). In U.S.patent application Ser. No. 10/124,800, the inventors also identified aThraustochytrium species as meeting the criteria for having a PUFA PKSsystem and then demonstrated that this organism was likely to containgenes with homology to Schizochytrium PUFA PKS genes by Southern blotanalysis. However, the isolation and determination of the structure ofsuch genes and the domain organization of the genes was not described inU.S. patent application Ser. No. 10/124,800. In the present invention,the inventors have now cloned and sequenced the full-length genomicsequence of homologous open reading frames (Orfs) in thisThraustochytrid of the genus Thraustochytrium (specifically,Thraustochytrium sp. 23B (ATCC 20892)), and have identified the domainscomprising the PUFA PKS system in this Thraustochytrium. Therefore, thepresent invention solves the above-mentioned problem of providingadditional PUFA PKS systems that have the flexibility for commercialuse. The Thraustochytrium PUFA PKS system is described in detail below.

The present invention also solves the above-identified problem forproduction of commercially valuable lipids enriched in a desired PUFA,such as EPA, by the present inventors' development of geneticallymodified microorganisms and methods for efficiently producing lipids(triacylglyerols (TAG) as well as membrane-associated phospholipids(PL)) enriched in PUFAs by manipulation of the polyketide synthase-likesystem that produces PUFAs in eukaryotes, including members of the orderThraustochytriales such as Schizochytrium and Thraustochytrium.Specifically, and by way of example, the present inventors describeherein a strain of Schizochytrium that has previously been optimized forcommercial production of oils enriched in PUFA, primarilydocosahexaenoic acid (DHA; C22:6 n-3) and docosapentaenoic acid (DPA;C22:5 n-6), and that will now be genetically modified such that EPA(C20:5 n-3) production (or other PUFA production) replaces the DHAproduction, without sacrificing the oil productivity characteristics ofthe organism. In addition, the present inventors describe herein thegenetic modification of Schizochytrium with PUFA PKS genes fromThraustochytrium to improve the DHA production by the Schizochytriumorganism, specifically by altering the ratio of DHA to DPA produced bythe microorganism through the modification of the PUFA PKS system. Theseare only a few examples of the technology encompassed by the invention,as the concepts of the invention can readily be applied to otherproduction organisms and other desired PUFAs as described in detailbelow.

In one embodiment, a PUFA PKS system according to the present inventioncomprises at least the following biologically active domains: (a) atleast two enoyl-ACP reductase (ER) domains; (b) at least six acylcarrier protein (ACP) domains; (c) at least two β-ketoacyl-ACP synthase(KS) domains; (d) at least one acyltransferase (AT) domain; (e) at leastone β-ketoacyl-ACP reductase (KR) domain; (f) at least two FabA-likeβ-hydroxyacyl-ACP dehydrase (DH) domains; (g) at least one chain lengthfactor (CLF) domain; and (h) at least one malonyl-CoA:ACPacyltransferase (MAT) domain. The functions of these domains aregenerally individually known in the art and will be described in detailbelow with regard to the PUFA PKS system of the present invention.

In another embodiment, the PUFA PKS system comprises at least thefollowing biologically active domains: (a) at least one enoyl-ACPreductase (ER) domain; (b) multiple acyl carrier protein (ACP) domains(at least from one to four, and preferably at least five, and morepreferably at least six, and even more preferably seven, eight, nine, ormore than nine); (c) at least two β-ketoacyl-ACP synthase (KS) domains;(d) at least one acyltransferase (AT) domain; (e) at least oneβ-ketoacyl-ACP reductase (KR) domain; (f) at least two FabA-likeβ-hydroxyacyl-ACP dehydrase (DH) domains; (g) at least one chain lengthfactor (CLF) domain; and (h) at least one malonyl-CoA:ACPacyltransferase (MAT) domain. Preferably, such a PUFA PKS system is anon-bacterial PUFA-PKS system.

In one embodiment, a PUFA PKS system of the present invention is anon-bacterial PUFA PKS system. In other words, in one embodiment, thePUFA PKS system of the present invention is isolated from an organismthat is not a bacterium, or is a homologue of, or derived from, a PUFAPKS system from an organism that is not a bacterium, such as a eukaryoteor an archaebacterium. Eukaryotes are separated from prokaryotes basedon the degree of differentiation of the cells, with eukaryotes havingmore highly differentiated cells and prokaryotes having lessdifferentiated cells. In general, prokaryotes do not possess a nuclearmembrane, do not exhibit mitosis during cell division, have only onechromosome, their cytoplasm contains 70S ribosomes, they do not possessany mitochondria, endoplasmic reticulum, chloroplasts, lysosomes orGolgi apparatus, their flagella (if present) consists of a singlefibril. In contrast, eukaryotes have a nuclear membrane, they do exhibitmitosis during cell division, they have many chromosomes, theircytoplasm contains 80S ribosomes, they do possess mitochondria,endoplasmic reticulum, chloroplasts (in algae), lysosomes and Golgiapparatus, and their flagella (if present) consists of many fibrils. Ingeneral, bacteria are prokaryotes, while algae, fungi, protist, protozoaand higher plants are eukaryotes.

The PUFA PKS systems of the marine bacteria (e.g., Shewanella sp. strainSCRC2738 and Vibrio marinus) are not the basis of the present invention,although the present invention does contemplate the use of domains fromthese bacterial PUFA PKS systems in conjunction with domains from thenon-bacterial PUFA PKS systems of the present invention. In addition,the present invention does contemplate the isolation and use of PUFA PKSgene sets (and proteins and domains encoded thereby) isolated from otherbacteria (e.g. Shewanella olleyana and Shewanella japonica) that will beparticularly suitable for use as sources of PUFA PKS genes for modifyingor combining with the non-bacterial PUFA PKS genes described herein toproduce hybrid constructs and genetically modified microorganisms andplants. For example, according to the present invention, geneticallymodified organisms can be produced which incorporate non-bacterial PUFAPKS functional domains with bacterial PUFA PKS functional domains, aswell as PKS functional domains or proteins from other PKS systems (typeI, type II, modular) or FAS systems. As discussed in more detail below,PUFA PKS genes from two species of Shewanella, namely Shewanellaolleyana or Shewanella japonica, are exemplary bacterial genes that arepreferred for use in genetically modified microorganisms, plants, andmethods of the invention. PUFA PKS systems (genes and the proteins anddomains encoded thereby) from such marine bacteria (e.g., Shewanellaolleyana or Shewanella japonica) are encompassed by the presentinvention as novel PUFA PKS sequences.

According to the present invention, the terms/phrases “Thraustochytrid”,“Thraustochytriales microorganism” and “microorganism of the orderThraustochytriales” can be used interchangeably and refer to any membersof the order Thraustochytriales, which includes both the familyThraustochytriaceae and the family Labyrinthulaceae. The terms“Labyrinthulid” and “Labyrinthulaceae” are used herein to specificallyrefer to members of the family Labyrinthulaceae. To specificallyreference Thraustochytrids that are members of the familyThraustochytriaceae, the term “Thraustochytriaceae” is used herein.Thus, for the present invention, members of the Labyrinthulids areconsidered to be included in the Thraustochytrids.

Developments have resulted in frequent revision of the taxonomy of theThraustochytrids. Taxonomic theorists generally place Thraustochytridswith the algae or algae-like protists. However, because of taxonomicuncertainty, it would be best for the purposes of the present inventionto consider the strains described in the present invention asThraustochytrids to include the following organisms: Order:Thraustochytriales; Family: Thraustochytriaceae (Genera:Thraustochytrium, Schizochytrium, Japonochytrium, Aplanochytrium, orElina) or Labyrinthulaceae (Genera Labyrinthula, Labyrinthuloides, orLabyrinthomyxa). Also, the following genera are sometimes included ineither family Thraustochytriaceae or Labyrinthulaceae: Althornia,Corallochytrium, Diplophyrys, and Pyrrhosorus), and for the purposes ofthis invention are encompassed by reference to a Thraustochytrid or amember of the order Thraustochytriales. It is recognized that at thetime of this invention, revision in the taxonomy of Thraustochytridsplaces the genus Labyrinthuloides in the family of Labyrinthulaceae andconfirms the placement of the two families Thraustochytriaceae andLabyrinthulaceae within the Stramenopile lineage. It is noted that theLabyrinthulaceae are sometimes commonly called labyrinthulids orlabyrinthula, or labyrinthuloides and the Thraustochytriaceae arecommonly called thraustochytrids, although, as discussed above, for thepurposes of clarity of this invention, reference to Thraustochytridsencompasses any member of the order Thraustochytriales and/or includesmembers of both Thraustochytriaceae and Labyrinthulaceae. Recenttaxonomic changes are summarized below.

Strains of certain unicellular microorganisms disclosed herein aremembers of the order Thraustochytriales. Thraustochytrids are marineeukaryotes with an evolving taxonomic history. Problems with thetaxonomic placement of the Thraustochytrids have been reviewed by Moss(1986), Bahnweb and Jackle (1986) and Chamberlain and Moss (1988).

For convenience purposes, the Thraustochytrids were first placed bytaxonomists with other colorless zoosporic eukaryotes in thePhycomycetes (algae-like fungi). The name Phycomycetes, however, waseventually dropped from taxonomic status, and the Thraustochytrids wereretained in the Oomycetes (the biflagellate zoosporic fungi). It wasinitially assumed that the Oomycetes were related to the heterokontalgae, and eventually a wide range of ultrastructural and biochemicalstudies, summarized by Barr (Barr, 1981, Biosystems 14:359-370)supported this assumption. The Oomycetes were in fact accepted byLeedale (Leedale, 1974, Taxon 23:261-270) and other phycologists as partof the heterokont algae. However, as a matter of convenience resultingfrom their heterotrophic nature, the Oomycetes and Thraustochytrids havebeen largely studied by mycologists (scientists who study fungi) ratherthan phycologists (scientists who study algae).

From another taxonomic perspective, evolutionary biologists havedeveloped two general schools of thought as to how eukaryotes evolved.One theory proposes an exogenous origin of membrane-bound organellesthrough a series of endosymbioses (Margulis, 1970, Origin of EukaryoticCells. Yale University Press, New Haven); e.g., mitochondria werederived from bacterial endosymbionts, chloroplasts from cyanophytes, andflagella from spirochaetes. The other theory suggests a gradualevolution of the membrane-bound organelles from the non-membrane-boundedsystems of the prokaryote ancestor via an autogenous process(Cavalier-Smith, 1975, Nature (Lond.) 256:462-468). Both groups ofevolutionary biologists however, have removed the Oomycetes andThraustochytrids from the fungi and place them either with thechromophyte algae in the kingdom Chromophyta (Cavalier-Smith, 1981,BioSystems 14:461-481) (this kingdom has been more recently expanded toinclude other protists and members of this kingdom are now calledStramenopiles) or with all algae in the kingdom Protoctista (Margulisand Sagen, 1985, Biosystems 18:141-147).

With the development of electron microscopy, studies on theultrastructure of the zoospores of two genera of Thraustochytrids,Thraustochytrium and Schizochytrium, (Perkins, 1976, pp. 279-312 in“Recent Advances in Aquatic Mycology” (ed. E. B. G. Jones), John Wiley &Sons, New York; Kazama, 1980, Can. J. Bot. 58:2434-2446; Barr, 1981,Biosystems 14:359-370) have provided good evidence that theThraustochytriaceae are only distantly related to the Oomycetes.Additionally, genetic data representing a correspondence analysis (aform of multivariate statistics) of 5-S ribosomal RNA sequences indicatethat Thraustochytriales are clearly a unique group of eukaryotes,completely separate from the fungi, and most closely related to the redand brown algae, and to members of the Oomycetes (Mannella, et al.,1987, Mol. Evol. 24:228-235). Most taxonomists have agreed to remove theThraustochytrids from the Oomycetes (Bartnicki-Garcia, 1987, pp. 389-403in “Evolutionary Biology of the Fungi” (eds. Rayner, A. D. M., Brasier,C. M. & Moore, D.), Cambridge University Press, Cambridge).

In summary, employing the taxonomic system of Cavalier-Smith(Cavalier-Smith, 1981, BioSystems 14:461-481, 1983; Cavalier-Smith,1993, Microbiol Rev. 57:953-994), the Thraustochytrids are classifiedwith the chromophyte algae in the kingdom Chromophyta (Stramenopiles).This taxonomic placement has been more recently reaffirmed byCavalier-Smith et al. using the 18s rRNA signatures of the Heterokontato demonstrate that Thraustochytrids are chromists not Fungi(Cavalier-Smith et al., 1994, Phil. Tran. Roy. Soc. London SeriesBioSciences 346:387-397). This places the Thraustochytrids in acompletely different kingdom from the fungi, which are all placed in thekingdom Eufungi.

Currently, there are 71 distinct groups of eukaryotic organisms(Patterson 1999) and within these groups four major lineages have beenidentified with some confidence: (1) Alveolates, (2) Stramenopiles, (3)a Land Plant-green algae-Rhodophyte_Glaucophyte (“plant”) clade and (4)an Opisthokont clade (Fungi and Animals). Formerly these four majorlineages would have been labeled Kingdoms but use of the “kingdom”concept is no longer considered useful by some researchers.

As noted by Armstrong, Stramenopile refers to three-parted tubularhairs, and most members of this lineage have flagella bearing suchhairs. Motile cells of the Stramenopiles (unicellular organisms, sperm,zoopores) are asymmetrical having two laterally inserted flagella, onelong, bearing three-parted tubular hairs that reverse the thrust of theflagellum, and one short and smooth. Formerly, when the group was lessbroad, the Stramenopiles were called Kingdom Chromista or the heterokont(=different flagella) algae because those groups consisted of the BrownAlgae or Phaeophytes, along with the yellow-green Algae, Golden-brownAlgae, Eustigmatophytes and Diatoms. Subsequently some heterotrophic,fungal-like organisms, the water molds, and labyrinthulids (slime netamoebas), were found to possess similar motile cells, so a group namereferring to photosynthetic pigments or algae became inappropriate.Currently, two of the families within the Stramenopile lineage are theLabyrinthulaceae and the Thraustochytriaceae. Historically, there havebeen numerous classification strategies for these unique microorganismsand they are often classified under the same order (i.e.,Thraustochytriales). Relationships of the members in these groups arestill developing. Porter and Leander have developed data based on 18Ssmall subunit ribosomal DNA indicating the thraustochytrid-labyrinthulidclade in monophyletic. However, the clade is supported by two branches;the first contains three species of Thraustochytrium and Ulkeniaprofunda, and the second includes three species of Labyrinthula, twospecies of Labyrinthuloides and Schizochytrium aggregatum.

The taxonomic placement of the Thraustochytrids as used in the presentinvention is therefore summarized below:

Kingdom: Chromophyta (Stramenopiles)

Phylum: Heterokonta

Order: Thraustochytriales (Thraustochytrids)

Family: Thraustochytriaceae or Labyrinthulaceae

Genera: Thraustochytrium, Schizochytrium, Japonochytrium,Aplanochytrium, Elina, Labyrinthula, Labyrinthuloides, orLabyrinthulomyxa

Some early taxonomists separated a few original members of the genusThraustochytrium (those with an amoeboid life stage) into a separategenus called Ulkenia. However it is now known that most, if not all,Thraustochytrids (including Thraustochytrium and Schizochytrium),exhibit amoeboid stages and as such, Ulkenia is not considered by someto be a valid genus. As used herein, the genus Thraustochytrium willinclude Ulkenia.

Despite the uncertainty of taxonomic placement within higherclassifications of Phylum and Kingdom, the Thraustochytrids remain adistinctive and characteristic grouping whose members remainclassifiable within the order Thraustochytriales.

Schizochytrium is a Thraustochytrid marine microorganism thataccumulates large quantities of triacylglycerols rich in DHA anddocosapentaenoic acid (DPA; 22:5 ω-6); e.g., 30% DHA+DPA by dry weight(Barclay et al., J. Appl. Phycol. 6, 123 (1994)). In eukaryotes thatsynthesize 20- and 22-carbon PUFAs by an elongation/desaturationpathway, the pools of 18-, 20- and 22-carbon intermediates arerelatively large so that in vivo labeling experiments using[¹⁴C]-acetate reveal clear precursor-product kinetics for the predictedintermediates (Gellerman et al., Biochim. Biophys. Acta 573:23 (1979)).Furthermore, radiolabeled intermediates provided exogenously to suchorganisms are converted to the final PUFA products. The presentinventors have shown that [1-¹⁴C]-acetate was rapidly taken up bySchizochytrium cells and incorporated into fatty acids, but at theshortest labeling time (1 min), DHA contained 31% of the label recoveredin fatty acids, and this percentage remained essentially unchangedduring the 10-15 min of [¹⁴C]-acetate incorporation and the subsequent24 hours of culture growth. Similarly, DPA represented 10% of the labelthroughout the experiment. There is no evidence for a precursor-productrelationship between 16- or 18-carbon fatty acids and the 22-carbonpolyunsaturated fatty acids. These results are consistent with rapidsynthesis of DHA from [¹⁴C]-acetate involving very small (possiblyenzyme-bound) pools of intermediates. A cell-free homogenate derivedfrom Schizochytrium cultures incorporated [1-¹⁴C]-malonyl-CoA into DHA,DPA, and saturated fatty acids. The same biosynthetic activities wereretained by a 100,000×g supernatant fraction but were not present in themembrane pellet. Thus, DHA and DPA synthesis in Schizochytrium does notinvolve membrane-bound desaturases or fatty acid elongation enzymes likethose described for other eukaryotes (Parker-Barnes et al., 2000, supra;Shanklin et al., 1998, supra). These fractionation data contrast withthose obtained from the Shewanella enzymes (See Metz et al., 2001,supra) and may indicate use of a different (soluble) acyl acceptormolecule, such as CoA, by the Schizochytrium enzyme. It is expected thatThraustochytrium will have a similar biochemistry.

In U.S. Pat. No. 6,566,583, a cDNA library from Schizochytrium wasconstructed and approximately 8500 random clones (ESTs) were sequenced.Sequences that exhibited homology to 8 of the 11 domains of theShewanella PKS genes shown in FIG. 2 were all identified at frequenciesof 0.2-0.5%. In U.S. Pat. No. 6,566,583, several cDNA clones fromSchizochytrium showing homology to the Shewanella PKS genes weresequenced, and various clones were assembled into nucleic acid sequencesrepresenting two partial open reading frames and one complete openreading frame.

Further sequencing of cDNA and genomic clones by the present inventorsallowed the identification of the full-length genomic sequence of eachof OrfA, OrfB and OrfC in Schizochytrium and the complete identificationof the domains in Schizochytrium with homology to those in Shewanella(see FIG. 2). These genes are described in detail in U.S. patentapplication Ser. No. 10/124,800, supra and are described in some detailbelow.

The present inventors have now identified, cloned, and sequenced thefull-length genomic sequence of homologous Orfs in a Thraustochytrid ofthe genus Thraustochytrium (specifically, Thraustochytrium sp. 23B (ATCC20892)) and have identified the domains comprising the PUFA PKS systemin this Thraustochytrium.

Based on the comparison of the domains of the PUFA PKS system ofSchizochytrium with the domains of the PUFA PKS system of Shewanella,clearly, the Schizochytrium genome encodes proteins that are highlysimilar to the proteins in Shewanella that are capable of catalyzing EPAsynthesis. The proteins in Schizochytrium constitute a PUFA PKS systemthat catalyzes DHA and DPA synthesis. Simple modification of thereaction scheme identified for Shewanella will allow for DHA synthesisin Schizochytrium. The homology between the prokaryotic Shewanella andeukaryotic Schizochytrium genes suggests that the PUFA PKS has undergonelateral gene transfer.

A similar comparison can be made for Thraustochytrium. In all cases,comparison of the Thraustochytrium 23B (Th. 23B) PUFA PKS proteins ordomains to other known sequences revealed that the closest match was oneof the Schizochytrium PUFA PKS proteins (OrfA, B or C, or a domaintherefrom) as described in U.S. patent application Ser. No. 10/124,800,supra. The next closest matches in all cases were to one of the PUFA PKSproteins from marine bacteria (Shewanella SCRC-2738, Shewanellaoneidensis, Photobacter profundum and Moritella marina) or from arelated system found in nitrogen fixing cyanobacteria (e.g., Nostocpunctiforme and Nostoc sp. PCC 7120). The products of the cyanobacterialenzyme systems lack double bonds and the proteins lack domains relatedto the DH domains implicated in cis double bond formation (i.e., theFabA related DH domains).

According to the present invention, the phrase “open reading frame” isdenoted by the abbreviation “Orf”. It is noted that the protein encodedby an open reading frame can also be denoted in all upper case lettersas “ORF” and a nucleic acid sequence for an open reading frame can alsobe denoted in all lower case letters as “orf”, but for the sake ofconsistency, the spelling “Orf” is preferentially used herein todescribe either the nucleic acid sequence or the protein encodedthereby. It will be obvious from the context of the usage of the termwhether a protein or nucleic acid sequence is referenced.

Schizochytrium PUFA PKS

FIG. 1 is a graphical representation of the three open reading framesfrom the Schizochytrium PUFA PKS system, and includes the domainstructure of this PUFA PKS system. As described in detail in U.S. patentapplication Ser. No. 10/124,800, the domain structure of each openreading frame is as follows:

Open Reading Frame A (OrfA):

The complete nucleotide sequence for OrfA is represented herein as SEQID NO:1. OrfA is a 8730 nucleotide sequence (not including the stopcodon) which encodes a 2910 amino acid sequence, represented herein asSEQ ID NO:2. Within OrfA are twelve domains: (a) one β-ketoacyl-ACPsynthase (KS) domain; (b) one malonyl-CoA:ACP acyltransferase (MAT)domain; (c) nine acyl carrier protein (ACP) domains; and (d) oneβ-ketoacyl-ACP reductase (KR) domain. The nucleotide sequence for OrfAhas been deposited with GenBank as Accession No. AF378327 (amino acidsequence Accession No. AAK728879).

The first domain in Schizochytrium OrfA is a β-ketoacyl-ACP synthase(KS) domain, also referred to herein as OrfA-KS. This domain iscontained within the nucleotide sequence spanning from a starting pointof between about positions 1 and 40 of SEQ ID NO:1 (OrfA) to an endingpoint of between about positions 1428 and 1500 of SEQ ID NO:1. Thenucleotide sequence containing the sequence encoding the OrfA-KS domainis represented herein as SEQ ID NO:7 (positions 1-1500 of SEQ ID NO:1).The amino acid sequence containing the KS domain spans from a startingpoint of between about positions 1 and 14 of SEQ ID NO:2 (OrfA) to anending point of between about positions 476 and 500 of SEQ ID NO:2. Theamino acid sequence containing the OrfA-KS domain is represented hereinas SEQ ID NO:8 (positions 1-500 of SEQ ID NO:2). It is noted that theOrfA-KS domain contains an active site motif: DXAC* (*acyl binding siteC₂₁₅).

According to the present invention, a domain or protein havingβ-ketoacyl-ACP synthase (KS) biological activity (function) ischaracterized as the enzyme that carries out the initial step of the FAS(and PKS) elongation reaction cycle. The term “β-ketoacyl-ACP synthase”can be used interchangeably with the terms “3-keto acyl-ACP synthase”,“β-keto acyl-ACP synthase”, and “keto-acyl ACP synthase”, and similarderivatives. The acyl group destined for elongation is linked to acysteine residue at the active site of the enzyme by a thioester bond.In the multi-step reaction, the acyl-enzyme undergoes condensation withmalonyl-ACP to form -ketoacyl-ACP, CO₂ and free enzyme. The KS plays akey role in the elongation cycle and in many systems has been shown topossess greater substrate specificity than other enzymes of the reactioncycle. For example, E. coli has three distinct KS enzymes—each with itsown particular role in the physiology of the organism (Magnuson et al.,Microbiol. Rev. 57, 522 (1993)). The two KS domains of the PUFA-PKSsystems could have distinct roles in the PUFA biosynthetic reactionsequence.

As a class of enzymes, KS's have been well characterized. The sequencesof many verified KS genes are known, the active site motifs have beenidentified and the crystal structures of several have been determined.Proteins (or domains of proteins) can be readily identified as belongingto the KS family of enzymes by homology to known KS sequences.

The second domain in OrfA is a malonyl-CoA:ACP acyltransferase (MAT)domain, also referred to herein as OrfA-MAT. This domain is containedwithin the nucleotide sequence spanning from a starting point of betweenabout positions 1723 and 1798 of SEQ ID NO:1 (OrfA) to an ending pointof between about positions 2805 and 3000 of SEQ ID NO:1. The nucleotidesequence containing the sequence encoding the OrfA-MAT domain isrepresented herein as SEQ ID NO:9 (positions 1723-3000 of SEQ ID NO:1).The amino acid sequence containing the MAT domain spans from a startingpoint of between about positions 575 and 600 of SEQ ID NO:2 (OrfA) to anending point of between about positions 935 and 1000 of SEQ ID NO:2. Theamino acid sequence containing the OrfA-MAT domain is represented hereinas SEQ ID NO:10 (positions 575-1000 of SEQ ID NO:2). It is noted thatthe OrfA-MAT domain contains an active site motif: GHS*XG (*acyl bindingsite S₇₀₆), represented herein as SEQ ID NO:11.

According to the present invention, a domain or protein havingmalonyl-CoA:ACP acyltransferase (MAT) biological activity (function) ischaracterized as one that transfers the malonyl moiety from malonyl-CoAto ACP. The term “malonyl-CoA:ACP acyltransferase” can be usedinterchangeably with “malonyl acyltransferase” and similar derivatives.In addition to the active site motif (GxSxG), these enzymes possess anextended motif (R and Q amino acids in key positions) that identifiesthem as MAT enzymes (in contrast to the AT domain of Schizochytrium OrfB). In some PKS systems (but not the PUFA PKS domain) MAT domains willpreferentially load methyl- or ethyl-malonate on to the ACP group (fromthe corresponding CoA ester), thereby introducing branches into thelinear carbon chain. MAT domains can be recognized by their homology toknown MAT sequences and by their extended motif structure.

Domains 3-11 of OrfA are nine tandem acyl carrier protein (ACP) domains,also referred to herein as OrfA-ACP (the first domain in the sequence isOrfA-ACP1, the second domain is OrfA-ACP2, the third domain isOrfA-ACP3, etc.). The first ACP domain, OrfA-ACP1, is contained withinthe nucleotide sequence spanning from about position 3343 to aboutposition 3600 of SEQ ID NO:1 (OrfA). The nucleotide sequence containingthe sequence encoding the OrfA-ACP1 domain is represented herein as SEQID NO:12 (positions 3343-3600 of SEQ ID NO:1). The amino acid sequencecontaining the first ACP domain spans from about position 1115 to aboutposition 1200 of SEQ ID NO:2. The amino acid sequence containing theOrfA-ACP1 domain is represented herein as SEQ ID NO:13 (positions1115-1200 of SEQ ID NO:2). It is noted that the OrfA-ACP1 domaincontains an active site motif: LGIDS* (*pantetheine binding motifS₁₁₅₇), represented herein by SEQ ID NO:14.

The nucleotide and amino acid sequences of all nine ACP domains arehighly conserved and therefore, the sequence for each domain is notrepresented herein by an individual sequence identifier. However, basedon the information disclosed herein, one of skill in the art can readilydetermine the sequence containing each of the other eight ACP domains(see discussion below).

All nine ACP domains together span a region of OrfA of from aboutposition 3283 to about position 6288 of SEQ ID NO:1, which correspondsto amino acid positions of from about 1095 to about 2096 of SEQ ID NO:2.The nucleotide sequence for the entire ACP region containing all ninedomains is represented herein as SEQ ID NO:16. The region represented bySEQ ID NO:16 includes the linker segments between individual ACPdomains. The repeat interval for the nine domains is approximately every330 nucleotides of SEQ ID NO:16 (the actual number of amino acidsmeasured between adjacent active site serines ranges from 104 to 116amino acids). Each of the nine ACP domains contains a pantetheinebinding motif LGIDS* (represented herein by SEQ ID NO:14), wherein S* isthe pantetheine binding site serine (S). The pantetheine binding siteserine (S) is located near the center of each ACP domain sequence. Ateach end of the ACP domain region and between each ACP domain is aregion that is highly enriched for proline (P) and alanine (A), which isbelieved to be a linker region. For example, between ACP domains 1 and 2is the sequence: APAPVKAAAPAAPVASAPAPA, represented herein as SEQ IDNO:15. The locations of the active site serine residues (i.e., thepantetheine binding site) for each of the nine ACP domains, with respectto the amino acid sequence of SEQ ID NO:2, are as follows: ACP1=S₁₁₅₇;ACP2=S₁₂₆₆; ACP3=S₁₃₇₇; ACP4=S₁₄₈₈; ACP5=S₁₆₀₄; ACP6=S₁₇₁₅; ACP7=S₁₈₁₉;ACP8=S₁₉₃₀; and ACP9=S₂₀₃₄. Given that the average size of an ACP domainis about 85 amino acids, excluding the linker, and about 110 amino acidsincluding the linker, with the active site serine being approximately inthe center of the domain, one of skill in the art can readily determinethe positions of each of the nine ACP domains in OrfA.

According to the present invention, a domain or protein having acylcarrier protein (ACP) biological activity (function) is characterized asbeing small polypeptides (typically, 80 to 100 amino acids long), thatfunction as carriers for growing fatty acyl chains via a thioesterlinkage to a covalently bound co-factor of the protein. They occur asseparate units or as domains within larger proteins. ACPs are convertedfrom inactive apo-forms to functional holo-forms by transfer of thephosphopantetheinyl moeity of CoA to a highly conserved serine residueof the ACP. Acyl groups are attached to ACP by a thioester linkage atthe free terminus of the phosphopantetheinyl moiety. ACPs can beidentified by labeling with radioactive pantetheine and by sequencehomology to known ACPs. The presence of variations of the abovementioned motif (LGIDS*) is also a signature of an ACP.

Domain 12 in OrfA is a β-ketoacyl-ACP reductase (KR) domain, alsoreferred to herein as OrfA-KR. This domain is contained within thenucleotide sequence spanning from a starting point of about position6598 of SEQ ID NO:1 to an ending point of about position 8730 of SEQ IDNO:1. The nucleotide sequence containing the sequence encoding theOrfA-KR domain is represented herein as SEQ ID NO:17 (positions6598-8730 of SEQ ID NO:1). The amino acid sequence containing the KRdomain spans from a starting point of about position 2200 of SEQ ID NO:2(OrfA) to an ending point of about position 2910 of SEQ ID NO:2. Theamino acid sequence containing the OrfA-KR domain is represented hereinas SEQ ID NO:18 (positions 2200-2910 of SEQ ID NO:2). Within the KRdomain is a core region with homology to short chainaldehyde-dehydrogenases (KR is a member of this family). This coreregion spans from about position 7198 to about position 7500 of SEQ IDNO:1, which corresponds to amino acid positions 2400-2500 of SEQ IDNO:2.

According to the present invention, a domain or protein havingβ-ketoacyl-ACP reductase (KR) activity is characterized as one thatcatalyzes the pyridine-nucleotide-dependent reduction of 3-ketoacylforms of ACP. The term “β-ketoacyl-ACP reductase” can be usedinterchangeably with the terms “ketoreductase”, “3-ketoacyl-ACPreductase”, “keto-acyl ACP reductase” and similar derivatives of theterm. It is the first reductive step in the de novo fatty acidbiosynthesis elongation cycle and a reaction often performed inpolyketide biosynthesis. Significant sequence similarity is observedwith one family of enoyl-ACP reductases (ER), the other reductase of FAS(but not the ER family present in the PUFA PKS system), and theshort-chain alcohol dehydrogenase family. Pfam analysis of the PUFA PKSregion indicated above reveals the homology to the short-chain alcoholdehydrogenase family in the core region. Blast analysis of the sameregion reveals matches in the core area to known KR enzymes as well asan extended region of homology to domains from the other characterizedPUFA PKS systems.

Open Reading Frame B (OrfB):

The complete nucleotide sequence for OrfB is represented herein as SEQID NO:3. OrfB is a 6177 nucleotide sequence (not including the stopcodon) which encodes a 2059 amino acid sequence, represented herein asSEQ ID NO:4. Within OrfB are four domains: (a) one β-ketoacyl-ACPsynthase (KS) domain; (b) one chain length factor (CLF) domain; (c) oneacyltransferase (AT) domain; and, (d) one enoyl-ACP reductase (ER)domain. The nucleotide sequence for OrfB has been deposited with GenBankas Accession No. AF378328 (amino acid sequence Accession No. AAK728880).

The first domain in OrfB is a β-ketoacyl-ACP synthase (KS) domain, alsoreferred to herein as OrfB-KS. This domain is contained within thenucleotide sequence spanning from a starting point of between aboutpositions 1 and 43 of SEQ ID NO:3 (OrfB) to an ending point of betweenabout positions 1332 and 1350 of SEQ ID NO:3. The nucleotide sequencecontaining the sequence encoding the OrfB-KS domain is representedherein as SEQ ID NO:19 (positions 1-1350 of SEQ ID NO:3). The amino acidsequence containing the KS domain spans from a starting point of betweenabout positions 1 and 15 of SEQ ID NO:4 (OrfB) to an ending point ofbetween about positions 444 and 450 of SEQ ID NO:4. The amino acidsequence containing the OrfB-KS domain is represented herein as SEQ IDNO:20 (positions 1-450 of SEQ ID NO:4). It is noted that the OrfB-KSdomain contains an active site motif: DXAC* (*acyl binding site C₁₉₆).KS biological activity and methods of identifying proteins or domainshaving such activity is described above.

The second domain in OrfB is a chain length factor (CLF) domain, alsoreferred to herein as OrfB-CLF. This domain is contained within thenucleotide sequence spanning from a starting point of between aboutpositions 1378 and 1402 of SEQ ID NO:3 (OrfB) to an ending point ofbetween about positions 2682 and 2700 of SEQ ID NO:3. The nucleotidesequence containing the sequence encoding the OrfB-CLF domain isrepresented herein as SEQ ID NO:21 (positions 1378-2700 of SEQ ID NO:3).The amino acid sequence containing the CLF domain spans from a startingpoint of between about positions 460 and 468 of SEQ ID NO:4 (OrfB) to anending point of between about positions 894 and 900 of SEQ ID NO:4. Theamino acid sequence containing the OrfB-CLF domain is represented hereinas SEQ ID NO:22 (positions 460-900 of SEQ ID NO:4). It is noted that theOrfB-CLF domain contains a KS active site motif without the acyl-bindingcysteine.

According to the present invention, a domain or protein is referred toas a chain length factor (CLF) based on the following rationale. The CLFwas originally described as characteristic of Type II (dissociatedenzymes) PKS systems and was hypothesized to play a role in determiningthe number of elongation cycles, and hence the chain length, of the endproduct. CLF amino acid sequences show homology to KS domains (and arethought to form heterodimers with a KS protein), but they lack theactive site cysteine. CLF's role in PKS systems is currentlycontroversial. New evidence (C. Bisang et al., Nature 401, 502 (1999))suggests a role in priming (providing the initial acyl group to beelongated) the PKS systems. In this role the CLF domain is thought todecarboxylate malonate (as malonyl-ACP), thus forming an acetate groupthat can be transferred to the KS active site. This acetate thereforeacts as the ‘priming’ molecule that can undergo the initial elongation(condensation) reaction. Homologues of the Type II CLF have beenidentified as ‘loading’ domains in some modular PKS systems. A domainwith the sequence features of the CLF is found in all currentlyidentified PUFA PKS systems and in each case is found as part of amultidomain protein.

The third domain in OrfB is an AT domain, also referred to herein asOrfB-AT. This domain is contained within the nucleotide sequencespanning from a starting point of between about positions 2701 and 3598of SEQ ID NO:3 (OrfB) to an ending point of between about positions 3975and 4200 of SEQ ID NO:3. The nucleotide sequence containing the sequenceencoding the OrfB-AT domain is represented herein as SEQ ID NO:23(positions 2701-4200 of SEQ ID NO:3). The amino acid sequence containingthe AT domain spans from a starting point of between about positions 901and 1200 of SEQ ID NO:4 (OrfB) to an ending point of between aboutpositions 1325 and 1400 of SEQ ID NO:4. The amino acid sequencecontaining the OrfB-AT domain is represented herein as SEQ ID NO:24(positions 901-1400 of SEQ ID NO:4). It is noted that the OrfB-AT domaincontains an active site motif of GxS*xG (*acyl binding site S₁₁₄₀) thatis characteristic of acyltransferase (AT) proteins.

An “acyltransferase” or “AT” refers to a general class of enzymes thatcan carry out a number of distinct acyl transfer reactions. The term“acyltransferase” can be used interchangeably with the term “acyltransferase”. The Schizochytrium domain shows good homology to a domainpresent in all of the other PUFA PKS systems currently examined and veryweak homology to some acyltransferases whose specific functions havebeen identified (e.g. to malonyl-CoA:ACP acyltransferase, MAT). In spiteof the weak homology to MAT, this AT domain is not believed to functionas a MAT because it does not possess an extended motif structurecharacteristic of such enzymes (see MAT domain description, above). Forthe purposes of this disclosure, the functions of the AT domain in aPUFA PKS system include, but are not limited to: transfer of the fattyacyl group from the OrfA ACP domain(s) to water (i.e. athioesterase—releasing the fatty acyl group as a free fatty acid),transfer of a fatty acyl group to an acceptor such as CoA, transfer ofthe acyl group among the various ACP domains, or transfer of the fattyacyl group to a lipophilic acceptor molecule (e.g. to lysophosphadicacid).

The fourth domain in OrfB is an ER domain, also referred to herein asOrfB-ER. This domain is contained within the nucleotide sequencespanning from a starting point of about position 4648 of SEQ ID NO:3(OrfB) to an ending point of about position 6177 of SEQ ID NO:3. Thenucleotide sequence containing the sequence encoding the OrfB-ER domainis represented herein as SEQ ID NO:25 (positions 4648-6177 of SEQ IDNO:3). The amino acid sequence containing the ER domain spans from astarting point of about position 1550 of SEQ ID NO:4 (OrfB) to an endingpoint of about position 2059 of SEQ ID NO:4. The amino acid sequencecontaining the OrfB-ER domain is represented herein as SEQ ID NO:26(positions 1550-2059 of SEQ ID NO:4).

According to the present invention, this domain has enoyl-ACP reductase(ER) biological activity. According to the present invention, the term“enoyl-ACP reductase” can be used interchangeably with “enoylreductase”, “enoyl ACP-reductase” and “enoyl acyl-ACP reductase”. The ERenzyme reduces the trans-double bond (introduced by the DH activity) inthe fatty acyl-ACP, resulting in fully saturating those carbons. The ERdomain in the PUFA-PKS shows homology to a newly characterized family ofER enzymes (Heath et al., Nature 406, 145 (2000)). Heath and Rockidentified this new class of ER enzymes by cloning a gene of interestfrom Streptococcus pneumoniae, purifying a protein expressed from thatgene, and showing that it had ER activity in an in vitro assay. Thesequence of the Schizochytrium ER domain of OrfB shows homology to theS. pneumoniae ER protein. All of the PUFA PKS systems currently examinedcontain at least one domain with very high sequence homology to theSchizochytrium ER domain. The Schizochytrium PUFA PKS system containstwo ER domains (one on OrfB and one on OrfC).

Open Reading Frame C (OrfC):

The complete nucleotide sequence for OrfC is represented herein as SEQID NO:5. OrfC is a 4509 nucleotide sequence (not including the stopcodon) which encodes a 1503 amino acid sequence, represented herein asSEQ ID NO:6. Within OrfC are three domains: (a) two FabA-likeβ-hydroxyacyl-ACP dehydrase (DH) domains; and (b) one enoyl-ACPreductase (ER) domain. The nucleotide sequence for OrfC has beendeposited with GenBank as Accession No. AF378329 (amino acid sequenceAccession No. AAK728881).

The first domain in OrfC is a DH domain, also referred to herein asOrfC-DH1. This is one of two DH domains in OrfC, and therefore isdesignated DH1. This domain is contained within the nucleotide sequencespanning from a starting point of between about positions 1 and 778 ofSEQ ID NO:5 (OrfC) to an ending point of between about positions 1233and 1350 of SEQ ID NO:5. The nucleotide sequence containing the sequenceencoding the OrfC-DH1 domain is represented herein as SEQ ID NO:27(positions 1-1350 of SEQ ID NO:5). The amino acid sequence containingthe DH1 domain spans from a starting point of between about positions 1and 260 of SEQ ID NO:6 (OrfC) to an ending point of between aboutpositions 411 and 450 of SEQ ID NO:6. The amino acid sequence containingthe OrfC-DH1 domain is represented herein as SEQ ID NO:28 (positions1-450 of SEQ ID NO:6).

According to the present invention, this domain has FabA-likeβ-hydroxyacyl-ACP dehydrase (DH) biological activity. The term“FabA-like β-hydroxyacyl-ACP dehydrase” can be used interchangeably withthe terms “FabA-like β-hydroxy acyl-ACP dehydrase”, “β-hydroxyacyl-ACPdehydrase”, “dehydrase” and similar derivatives. The characteristics ofboth the DH domains (see below for DH 2) in the PUFA PKS systems havebeen described in the preceding sections. This class of enzyme removesHOH from a β-ketoacyl-ACP and leaves a trans double bond in the carbonchain. The DH domains of the PUFA PKS systems show homology to bacterialDH enzymes associated with their FAS systems (rather than to the DHdomains of other PKS systems). A subset of bacterial DH's, the FabA-likeDH's, possesses cis-trans isomerase activity (Heath et al., J. Biol.Chem., 271, 27795 (1996)). It is the homologies to the FabA-like DH'sthat indicate that one or both of the DH domains is responsible forinsertion of the cis double bonds in the PUFA PKS products.

The second domain in OrfC is a DH domain, also referred to herein asOrfC-DH2. This is the second of two DH domains in OrfC, and therefore isdesignated DH2. This domain is contained within the nucleotide sequencespanning from a starting point of between about positions 1351 and 2437of SEQ ID NO:5 (OrfC) to an ending point of between about positions 2607and 2850 of SEQ ID NO:5. The nucleotide sequence containing the sequenceencoding the OrfC-DH2 domain is represented herein as SEQ ID NO:29(positions 1351-2850 of SEQ ID NO:5). The amino acid sequence containingthe DH2 domain spans from a starting point of between about positions451 and 813 of SEQ ID NO:6 (OrfC) to an ending point of between aboutpositions 869 and 950 of SEQ ID NO:6. The amino acid sequence containingthe OrfC-DH2 domain is represented herein as SEQ ID NO:30 (positions451-950 of SEQ ID NO:6). DH biological activity has been describedabove.

The third domain in OrfC is an ER domain, also referred to herein asOrfC-ER. This domain is contained within the nucleotide sequencespanning from a starting point of about position 2998 of SEQ ID NO:5(OrfC) to an ending point of about position 4509 of SEQ ID NO:5. Thenucleotide sequence containing the sequence encoding the OrfC-ER domainis represented herein as SEQ ID NO:31 (positions 2998-4509 of SEQ IDNO:5). The amino acid sequence containing the ER domain spans from astarting point of about position 1000 of SEQ ID NO:6 (OrfC) to an endingpoint of about position 1502 of SEQ ID NO:6. The amino acid sequencecontaining the OrfC-ER domain is represented herein as SEQ ID NO:32(positions 1000-1502 of SEQ ID NO:6). ER biological activity has beendescribed above.

Thraustochytrium 23B PUFA PKS

Th. 23B Open Reading Frame A (OrfA):

The complete nucleotide sequence for Th. 23B OrfA is represented hereinas SEQ ID NO:38. SEQ ID NO:38 encodes the following domains in Th. 23BOrfA: (a) one β-ketoacyl-ACP synthase (KS) domain; (b) onemalonyl-CoA:ACP acyltransferase (MAT) domain; (c) eight acyl carrierprotein (ACP) domains; and (d) one β-ketoacyl-ACP reductase (KR) domain.This domain organization is the same as is present in Schizochytrium OrfA (SEQ ID NO:1) with the exception that the Th. 23B Orf A has 8 adjacentACP domains, while Schizochytrium Orf A has 9 adjacent ACP domains. Th.23B OrfA is a 8433 nucleotide sequence (not including the stop codon)which encodes a 2811 amino acid sequence, represented herein as SEQ IDNO:39. The Th. 23B OrfA amino acid sequence (SEQ ID NO:39) was comparedwith known sequences in a standard BLAST search (BLAST parameters:Blastp, low complexity filter Off, program-BLOSUM62, Gap cost-Existence:11, Extension 1; (BLAST described in Altschul, S. F., Madden, T. L.,Schääffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J.(1997) “Gapped BLAST and PSI-BLAST: a new generation of protein databasesearch programs.” Nucleic Acids Res. 25:3389-3402, incorporated hereinby reference in its entirety))). At the amino acid level, the sequenceswith the greatest degree of homology to Th. 23B OrfA was SchizochytriumOrf A (gb AAK72879.1) (SEQ ID NO:2). The alignment extends over theentire query but is broken into 2 pieces (due to the difference innumbers of ACP repeats). SEQ ID NO:39 first aligns at positions 6through 1985 (including 8 ACP domains) with SEQ ID NO:2 and shows asequence identity to SEQ ID NO:2 of 54% over 2017 amino acids. SEQ IDNO:39 also aligns at positions 980 through 2811 with SEQ ID NO:2 andshows a sequence identity to SEQ ID NO:2 of 43% over 1861 amino acids.In this second alignment, the match is evident for the Th. 23B 8×ACPs inthe regions of the conserved pantetheine attachment site motif, but isvery poor over the 1st Schizochytrium ACP domain (i.e., there is not a9^(th) ACP domain in the Th. 23B query sequence, but the Blastp outputunder theses conditions attempts to align them anyway). SEQ ID NO:39shows the next closest identity with sequences from Shewanellaoneidensis (Accession No. NP_(—)717214) and Photobacter profundum(Accession No. AAL01060).

The first domain in Th. 23B OrfA is a KS domain, also referred to hereinas Th. 23B OrfA-KS. KS domain function has been described in detailabove. This domain is contained within the nucleotide sequence spanningfrom about position 1 to about position 1500 of SEQ ID NO:38,represented herein as SEQ ID NO:40. The amino acid sequence containingthe Th. 23B KS domain is a region of SEQ ID NO:39 spanning from aboutposition 1 to about position 500 of SEQ ID NO:39, represented herein asSEQ ID NO:41. This region of SEQ ID NO:39 has a Pfam match to FabB(β-ketoacyl-ACP synthase) spanning from position 1 to about position 450of SEQ ID NO:39 (also positions 1 to about 450 of SEQ ID NO:41). It isnoted that the Th. 23B OrfA-KS domain contains an active site motif:DXAC* (*acyl binding site C₂₀₇). Also, a characteristic motif at the endof the Th. 23B KS region, GFGG, is present in positions 453-456 of SEQID NO:39 (also positions 453-456 of SEQ ID NO:41). The amino acidsequence spanning positions 1-500 of SEQ ID NO:39 is about 79% identicalto Schizochytrium OrfA (SEQ ID NO:2) over 496 amino acids. The aminoacid sequence spanning positions 1-450 of SEQ ID NO:39 is about 81%identical to Schizochytrium OrfA (SEQ ID NO:2) over 446 amino acids.

The second domain in Th. 23B OrfA is a MAT domain, also referred toherein as Th. 23B OrfA-MAT. MAT domain function has been described indetail above. This domain is contained within the nucleotide sequencespanning from between about position 1503 and about position 3000 of SEQID NO:38, represented herein as SEQ ID NO:42. The amino acid sequencecontaining the Th. 23B MAT domain is a region of SEQ ID NO:39 spanningfrom about position 501 to about position 1000, represented herein bySEQ ID NO:43. This region of SEQ ID NO:39 has a Pfam match to FabD(malonyl-CoA:ACP acyltransferase) spanning from about position 580 toabout position 900 of SEQ ID NO:39 (positions 80-400 of SEQ ID NO:43).It is noted that the Th. 23B OrfA-MAT domain contains an active sitemotif: GHS*XG (*acyl binding site S₆₉₇), represented by positions695-699 of SEQ ID NO:39. The amino acid sequence spanning positions501-1000 of SEQ ID NO:39 is about 46% identical to Schizochytrium OrfA(SEQ ID NO:2) over 481 amino acids. The amino acid sequence spanningpositions 580-900 of SEQ ID NO:39 is about 50% identical toSchizochytrium OrfA (SEQ ID NO:2) over 333 amino acids.

Domains 3-10 of Th. 23B OrfA are eight tandem ACP domains, also referredto herein as Th. 23B OrfA-ACP (the first domain in the sequence isOrfA-ACP1, the second domain is OrfA-ACP2, the third domain isOrfA-ACP3, etc.). The function of ACP domains has been described indetail above. The first Th. 23B ACP domain, Th. 23B OrfA-ACP1, iscontained within the nucleotide sequence spanning from about position3205 to about position 3555 of SEQ ID NO:38 (OrfA), represented hereinas SEQ ID NO:44. The amino acid sequence containing the first Th. 23BACP domain is a region of SEQ ID NO:39 spanning from about position 1069to about position 1185 of SEQ ID NO:39, represented herein by SEQ IDNO:45. The amino acid sequence spanning positions 1069-1185 of SEQ IDNO:39 is about 65% identical to Schizochytrium OrfA (SEQ ID NO:2) over85 amino acids. Th. 23B OrfA-ACP1 has a similar identity to any one ofthe nine ACP domains in Schizochytrium OrfA.

The eight ACP domains in Th. 23B OrfA are adjacent to one another andcan be identified by the presence of the phosphopantetheine binding sitemotif, LGXDS* (represented by SEQ ID NO:46), wherein the S* is thephosphopantetheine attachment site. The amino acid position of each ofthe eight S* sites, with reference to SEQ ID NO:39, are 1128 (ACP1),1244 (ACP2), 1360 (ACP3), 1476 (ACP4), 1592 (ACP5), 1708 (ACP6), 1824(ACP7) and 1940 (ACP8). The nucleotide and amino acid sequences of alleight Th. 23B ACP domains are highly conserved and therefore, thesequence for each domain is not represented herein by an individualsequence identifier. However, based on the information disclosed herein,one of skill in the art can readily determine the sequence containingeach of the other seven ACP domains in SEQ ID NO:38 and SEQ ID NO:39.

All eight Th. 23B ACP domains together span a region of Th. 23B OrfA offrom about position 3205 to about position 5994 of SEQ ID NO:38, whichcorresponds to amino acid positions of from about 1069 to about 1998 ofSEQ ID NO:39. The nucleotide sequence for the entire ACP regioncontaining all eight domains is represented herein as SEQ ID NO:47. SEQID NO:47 encodes an amino acid sequence represented herein by SEQ IDNO:48. SEQ ID NO:48 includes the linker segments between individual ACPdomains. The repeat interval for the eight domains is approximatelyevery 116 amino acids of SEQ ID NO:48, and each domain can be consideredto consist of about 116 amino acids centered on the active site motif(described above). It is noted that the linker regions between the nineadjacent ACP domains in OrfA in Schizochytrium are highly enriched inproline and alanine residues, while the linker regions between the eightadjacent ACP domains in OrfA of Thraustochytrium are highly enriched inserine residues (and not proline or alanine residues).

The last domain in Th. 23B OrfA is a KR domain, also referred to hereinas Th. 23B OrfA-KR. KR domain function has been discussed in detailabove. This domain is contained within the nucleotide sequence spanningfrom between about position 6001 to about position 8433 of SEQ ID NO:38,represented herein by SEQ ID NO:49. The amino acid sequence containingthe Th. 23B KR domain is a region of SEQ ID NO:39 spanning from aboutposition 2001 to about position 2811 of SEQ ID NO:39, represented hereinby SEQ ID NO:50. This region of SEQ ID NO:39 has a Pfam match to FabG(β-ketoacyl-ACP reductase) spanning from about position 2300 to about2550 of SEQ ID NO:39 (positions 300-550 of SEQ ID NO:50). The amino acidsequence spanning positions 2001-2811 of SEQ ID NO:39 is about 40%identical to Schizochytrium OrfA (SEQ ID NO:2) over 831 amino acids. Theamino acid sequence spanning positions 2300-2550 of SEQ ID NO:39 isabout 51% identical to Schizochytrium OrfA (SEQ ID NO:2) over 235 aminoacids.

Th. 23B Open Reading Frame B (Or/B):

The complete nucleotide sequence for Th. 23B OrfB is represented hereinas SEQ ID NO:51. SEQ ID NO:51 encodes the following domains in Th. 23BOrfB: (a) one β-ketoacyl-ACP synthase (KS) domain; (b) one chain lengthfactor (CLF) domain; (c) one acyltransferase (AT) domain; and, (d) oneenoyl-ACP reductase (ER) domain. This domain organization is the same asin Schizochytrium Orf B (SEQ ID NO:3) with the exception that the linkerregion between the AT and ER domains of the Schizochytrium protein islonger than that of Th. 23B by about 50-60 amino acids. Also, thislinker region in Schizochytrium has a specific area that is highlyenriched in serine residues (it contains 15 adjacent serine residues, inaddition to other serines in the region), whereas the correspondinglinker region in Th. 23B OrfB is not enriched in serine residues. Thisdifference in the AT/ER linker region most likely accounts for a breakin the alignment between Schizochytrium OrfB and Th. 23B OrfB at thestart of this region.

Th. 23B OrfB is a 5805 nucleotide sequence (not including the stopcodon) which encodes a 1935 amino acid sequence, represented herein asSEQ ID NO:52. The Th. 23B OrfB amino acid sequence (SEQ ID NO:52) wascompared with known sequences in a standard BLAST search (BLASTparameters: Blastp, low complexity filter Off, program-BLOSUM62, Gapcost-Existence: 11, Extension 1; (BLAST described in Altschul, S. F.,Madden, T. L., Schääffer, A. A., Zhang, J., Zhang, Z., Miller, W. &Lipman, D. J. (1997) “Gapped BLAST and PSI-BLAST: a new generation ofprotein database search programs.” Nucleic Acids Res. 25:3389-3402,incorporated herein by reference in its entirety))). At the amino acidlevel, the sequences with the greatest degree of homology to Th. 23BOrfB were Schizochytrium Orf B (gb AAK72880.1) (SEQ ID NO:4), over mostof OrfB; and Schizochytrium OrfC (gb AAK728881.1) (SEQ ID NO:6), overthe last domain (the alignment is broken into 2 pieces, as mentionedabove). SEQ ID NO:52 first aligns at positions 10 through about 1479(including the KS, CLF and AT domains) with SEQ ID NO:4 and shows asequence identity to SEQ ID NO:4 of 52% over 1483 amino acids. SEQ IDNO:52 also aligns at positions 1491 through 1935 (including the ERdomain) with SEQ ID NO:6 and shows a sequence identity to SEQ ID NO:4 of64% over 448 amino acids.

The first domain in the Th. 23B OrfB is a KS domain, also referred toherein as Th. 23B OrfB-KS. KS domain function has been described indetail above. This domain is contained within the nucleotide sequencespanning from between about position 1 and about position 1500 of SEQ IDNO:51 (Th. 23B OrfB), represented herein as SEQ ID NO:53. The amino acidsequence containing the Th. 23B KS domain is a region of SEQ ID NO: 52spanning from about position 1 to about position 500 of SEQ ID NO:52,represented herein as SEQ ID NO:54. This region of SEQ ID NO:52 has aPfam match to FabB (β-ketoacyl-ACP synthase) spanning from aboutposition 1 to about position 450 (positions 1-450 of SEQ ID NO:54). Itis noted that the Th. 23B OrfB-KS domain contains an active site motif:DXAC*, where C* is the site of acyl group attachment and wherein the C*is at position 201 of SEQ ID NO:52. Also, a characteristic motif at theend of the KS region, GFGG is present in amino acid positions 434-437 ofSEQ ID NO:52. The amino acid sequence spanning positions 1-500 of SEQ IDNO:52 is about 64% identical to Schizochytrium OrfB (SEQ ID NO:4) over500 amino acids. The amino acid sequence spanning positions 1-450 of SEQID NO:52 is about 67% identical to Schizochytrium OrfB (SEQ ID NO:4)over 442 amino acids.

The second domain in Th. 23B OrfB is a CLF domain, also referred toherein as Th. 23B OrfB-CLF. CLF domain function has been described indetail above. This domain is contained within the nucleotide sequencespanning from between about position 1501 and about position 3000 of SEQID NO:51 (OrfB), represented herein as SEQ ID NO:55. The amino acidsequence containing the CLF domain is a region of SEQ ID NO: 52 spanningfrom about position 501 to about position 1000 of SEQ ID NO:52,represented herein as SEQ ID NO:56. This region of SEQ ID NO:52 has aPfam match to FabB (β-ketoacyl-ACP synthase) spanning from aboutposition 550 to about position 910 (positions 50-410 of SEQ ID NO:56).Although CLF has homology to KS proteins, it lacks an active sitecysteine to which the acyl group is attached in KS proteins. The aminoacid sequence spanning positions 501-1000 of SEQ ID NO:52 is about 49%identical to Schizochytrium OrfB (SEQ ID NO:4) over 517 amino acids. Theamino acid sequence spanning positions 550-910 of SEQ ID NO:52 is about54% identical to Schizochytrium OrfB (SEQ ID NO:4) over 360 amino acids.

The third domain in Th. 23B OrfB is an AT domain, also referred toherein as Th. 23B OrfB-AT. AT domain function has been described indetail above. This domain is contained within the nucleotide sequencespanning from between about position 3001 and about position 4500 of SEQID NO:51 (Th. 23B OrfB), represented herein as SEQ ID NO:58. The aminoacid sequence containing the Th. 23B AT domain is a region of SEQ ID NO:52 spanning from about position 1001 to about position 1500 of SEQ IDNO:52, represented herein as SEQ ID NO:58. This region of SEQ ID NO:52has a Pfam match to FabD (malonyl-CoA:ACP acyltransferase) spanning fromabout position 1100 to about position 1375 (positions 100-375 of SEQ IDNO:58). Although this AT domain of the PUFA synthases has homology toMAT proteins, it lacks the extended motif of the MAT (key arginine andglutamine residues) and it is not thought to be involved in malonyl-CoAtransfers. The GXS*XG motif of acyltransferases is present, with the S*being the site of acyl attachment and located at position 1123 withrespect to SEQ ID NO:52. The amino acid sequence spanning positions1001-1500 of SEQ ID NO:52 is about 44% identical to Schizochytrium OrfB(SEQ ID NO:4) over 459 amino acids. The amino acid sequence spanningpositions 1100-1375 of SEQ ID NO:52 is about 45% identical toSchizochytrium OrfB (SEQ ID NO:4) over 283 amino acids.

The fourth domain in Th. 23B OrfB is an ER domain, also referred toherein as Th. 23B OrfB-ER. ER domain function has been described indetail above. This domain is contained within the nucleotide sequencespanning from between about position 4501 and about position 5805 of SEQID NO:51 (OrfB), represented herein as SEQ ID NO:59. The amino acidsequence containing the Th. 23B ER domain is a region of SEQ ID NO: 52spanning from about position 1501 to about position 1935 of SEQ IDNO:52, represented herein as SEQ ID NO:60. This region of SEQ ID NO:52has a Pfam match to a family of dioxygenases related to 2-nitropropanedioxygenases spanning from about position 1501 to about position 1810(positions 1-310 of SEQ ID NO:60). That this domain functions as an ERcan be further predicted due to homology to a newly characterized ERenzyme from Streptococcus pneumoniae. The amino acid sequence spanningpositions 1501-1935 of SEQ ID NO:52 is about 66% identical toSchizochytrium OrfB (SEQ ID NO:4) over 433 amino acids. The amino acidsequence spanning positions 1501-1810 of SEQ ID NO:52 is about 70%identical to Schizochytrium OrfB (SEQ ID NO:4) over 305 amino acids.

Th. 23B Open Reading Frame C (OrfC):

The complete nucleotide sequence for Th. 23B OrfC is represented hereinas SEQ ID NO:61. SEQ ID NO:61 encodes the following domains in Th. 23BOrfC: (a) two FabA-like β-hydroxyacyl-ACP dehydrase (DH) domains, bothwith homology to the FabA protein (an enzyme that catalyzes thesynthesis of trans-2-decenoyl-ACP and the reversible isomerization ofthis product to cis-3-decenoyl-ACP); and (b) one enoyl-ACP reductase(ER) domain with high homology to the ER domain of Schizochytrium OrfB.This domain organization is the same as in Schizochytrium Orf C (SEQ IDNO:5).

Th. 23B OrfC is a 4410 nucleotide sequence (not including the stopcodon) which encodes a 1470 amino acid sequence, represented herein asSEQ ID NO:62. The Th. 23B OrfC amino acid sequence (SEQ ID NO:62) wascompared with known sequences in a standard BLAST search (BLASTparameters: Blastp, low complexity filter Off, program-BLOSUM62, Gapcost-Existence: 11, Extension 1; (BLAST described in Altschul, S. F.,Madden, T. L., Schääffer, A. A., Zhang, J., Zhang, Z., Miller, W. &Lipman, D. J. (1997) “Gapped BLAST and PSI-BLAST: a new generation ofprotein database search programs.” Nucleic Acids Res. 25:3389-3402,incorporated herein by reference in its entirety))). At the amino acidlevel, the sequences with the greatest degree of homology to Th. 23BOrfC was Schizochytrium OrfC (gb AAK728881.1) (SEQ ID NO:6). SEQ IDNO:52 is 66% identical to Schizochytrium OrfC (SEQ ID NO:6).

The first domain in Th. 23B OrfC is a DH domain, also referred to hereinas Th. 23B OrfC-DH1. DH domain function has been described in detailabove. This domain is contained within the nucleotide sequence spanningfrom between about position 1 to about position 1500 of SEQ ID NO:61(OrfC), represented herein as SEQ ID NO:63. The amino acid sequencecontaining the Th. 23B DH1 domain is a region of SEQ ID NO: 62 spanningfrom about position 1 to about position 500 of SEQ ID NO:62, representedherein as SEQ ID NO:64. This region of SEQ ID NO:62 has a Pfam match toFabA, as mentioned above, spanning from about position 275 to aboutposition 400 (positions 275-400 of SEQ ID NO:64). The amino acidsequence spanning positions 1-500 of SEQ ID NO:62 is about 66% identicalto Schizochytrium OrfC (SEQ ID NO:6) over 526 amino acids. The aminoacid sequence spanning positions 275-400 of SEQ ID NO:62 is about 81%identical to Schizochytrium OrfC (SEQ ID NO:6) over 126 amino acids.

The second domain in Th. 23B OrfC is also a DH domain, also referred toherein as Th. 23B OrfC-DH2. This is the second of two DH domains inOrfC, and therefore is designated DH2. This domain is contained withinthe nucleotide sequence spanning from between about position 1501 toabout 3000 of SEQ ID NO:61 (OrfC), represented herein as SEQ ID NO:65.The amino acid sequence containing the Th. 23B DH2 domain is a region ofSEQ ID NO: 62 spanning from about position 501 to about position 1000 ofSEQ ID NO:62, represented herein as SEQ ID NO:66. This region of SEQ IDNO:62 has a Pfam match to FabA, as mentioned above, spanning from aboutposition 800 to about position 925 (positions 300-425 of SEQ ID NO:66).The amino acid sequence spanning positions 501-1000 of SEQ ID NO:62 isabout 56% identical to Schizochytrium OrfC (SEQ ID NO:6) over 518 aminoacids. The amino acid sequence spanning positions 800-925 of SEQ IDNO:62 is about 58% identical to Schizochytrium OrfC (SEQ ID NO:6) over124 amino acids.

The third domain in Th. 23B OrfC is an ER domain, also referred toherein as Th. 23B OrfC-ER. ER domain function has been described indetail above. This domain is contained within the nucleotide sequencespanning from between about position 3001 to about position 4410 of SEQID NO:61 (OrfC), represented herein as SEQ ID NO:67. The amino acidsequence containing the Th. 23B ER domain is a region of SEQ ID NO: 62spanning from about position 1001 to about position 1470 of SEQ IDNO:62, represented herein as SEQ ID NO:68. This region of SEQ ID NO:62has a Pfam match to the dioxygenases related to 2-nitropropanedioxygenases, as mentioned above, spanning from about position 1025 toabout position 1320 (positions 25-320 of SEQ ID NO:68). This domainfunction as an ER can also be predicted due to homology to a newlycharacterized ER enzyme from Streptococcus pneumoniae. The amino acidsequence spanning positions 1001-1470 of SEQ ID NO:62 is about 75%identical to Schizochytrium OrfB (SEQ ID NO:4) over 474 amino acids. Theamino acid sequence spanning positions 1025-1320 of SEQ ID NO:62 isabout 81% identical to Schizochytrium OrfB (SEQ ID NO:4) over 296 aminoacids.

One embodiment of the present invention relates to an isolated proteinor domain from a non-bacterial PUFA PKS system, a homologue thereof,and/or a fragment thereof. Also included in the invention are isolatednucleic acid molecules encoding any of the proteins, domains or peptidesdescribed herein (discussed in detail below). According to the presentinvention, an isolated protein or peptide, such as a protein or peptidefrom a PUFA PKS system, is a protein or a fragment thereof (including apolypeptide or peptide) that has been removed from its natural milieu(i.e., that has been subject to human manipulation) and can includepurified proteins, partially purified proteins, recombinantly producedproteins, and synthetically produced proteins, for example. As such,“isolated” does not reflect the extent to which the protein has beenpurified. Preferably, an isolated protein of the present invention isproduced recombinantly. An isolated peptide can be producedsynthetically (e.g., chemically, such as by peptide synthesis) orrecombinantly. In addition, and by way of example, a “ThraustochytriumPUFA PKS protein” refers to a PUFA PKS protein (generally including ahomologue of a naturally occurring PUFA PKS protein) from aThraustochytrium microorganism, or to a PUFA PKS protein that has beenotherwise produced from the knowledge of the structure (e.g., sequence),and perhaps the function, of a naturally occurring PUFA PKS protein fromThraustochytrium. In other words, general reference to aThraustochytrium PUFA PKS protein includes any PUFA PKS protein that hassubstantially similar structure and function of a naturally occurringPUFA PKS protein from Thraustochytrium or that is a biologically active(i.e., has biological activity) homologue of a naturally occurring PUFAPKS protein from Thraustochytrium as described in detail herein. Assuch, a Thraustochytrium PUFA PKS protein can include purified,partially purified, recombinant, mutated/modified and syntheticproteins. The same description applies to reference to other proteins orpeptides described herein, such as the PUFA PKS proteins and domainsfrom Schizochytrium or from other microorganisms.

According to the present invention, the terms “modification” and“mutation” can be used interchangeably, particularly with regard to themodifications/mutations to the primary amino acid sequences of a proteinor peptide (or nucleic acid sequences) described herein. The term“modification” can also be used to describe post-translationalmodifications to a protein or peptide including, but not limited to,methylation, farnesylation, carboxymethylation, geranyl geranylation,glycosylation, phosphorylation, acetylation, myristoylation,prenylation, palmitation, and/or amidation. Modifications can alsoinclude, for example, complexing a protein or peptide with anothercompound. Such modifications can be considered to be mutations, forexample, if the modification is different than the post-translationalmodification that occurs in the natural, wild-type protein or peptide.

As used herein, the term “homologue” is used to refer to a protein orpeptide which differs from a naturally occurring protein or peptide(i.e., the “prototype” or “wild-type” protein) by one or more minormodifications or mutations to the naturally occurring protein orpeptide, but which maintains the overall basic protein and side chainstructure of the naturally occurring form (i.e., such that the homologueis identifiable as being related to the wild-type protein). Such changesinclude, but are not limited to: changes in one or a few amino acid sidechains; changes one or a few amino acids, including deletions (e.g., atruncated version of the protein or peptide) insertions and/orsubstitutions; changes in stereochemistry of one or a few atoms; and/orminor derivatizations, including but not limited to: methylation,farnesylation, geranyl geranylation, glycosylation, carboxymethylation,phosphorylation, acetylation, myristoylation, prenylation, palmitation,and/or amidation. A homologue can have either enhanced, decreased, orsubstantially similar properties as compared to the naturally occurringprotein or peptide. Preferred homologues of a PUFA PKS protein or domainare described in detail below. It is noted that homologues can includesynthetically produced homologues, naturally occurring allelic variantsof a given protein or domain, or homologous sequences from organismsother than the organism from which the reference sequence was derived.

Conservative substitutions typically include substitutions within thefollowing groups: glycine and alanine; valine, isoleucine and leucine;aspartic acid, glutamic acid, asparagine, and glutamine; serine andthreonine; lysine and arginine; and phenylalanine and tyrosine.Substitutions may also be made on the basis of conserved hydrophobicityor hydrophilicity (Kyte and Doolittle, J. Mol. Biol. (1982) 157:105-132), or on the basis of the ability to assume similar polypeptidesecondary structure (Chou and Fasman, Adv. Enzymol. (1978) 47: 45-148,1978).

Homologues can be the result of natural allelic variation or naturalmutation. A naturally occurring allelic variant of a nucleic acidencoding a protein is a gene that occurs at essentially the same locus(or loci) in the genome as the gene which encodes such protein, butwhich, due to natural variations caused by, for example, mutation orrecombination, has a similar but not identical sequence. Allelicvariants typically encode proteins having similar activity to that ofthe protein encoded by the gene to which they are being compared. Oneclass of allelic variants can encode the same protein but have differentnucleic acid sequences due to the degeneracy of the genetic code.Allelic variants can also comprise alterations in the 5′ or 3′untranslated regions of the gene (e.g., in regulatory control regions).Allelic variants are well known to those skilled in the art.

Homologues can be produced using techniques known in the art for theproduction of proteins including, but not limited to, directmodifications to the isolated, naturally occurring protein, directprotein synthesis, or modifications to the nucleic acid sequenceencoding the protein using, for example, classic or recombinant DNAtechniques to effect random or targeted mutagenesis.

Modifications or mutations in protein homologues, as compared to thewild-type protein, either increase, decrease, or do not substantiallychange, the basic biological activity of the homologue as compared tothe naturally occurring (wild-type) protein. In general, the biologicalactivity or biological action of a protein refers to any function(s)exhibited or performed by the protein that is ascribed to the naturallyoccurring form of the protein as measured or observed in vivo (i.e., inthe natural physiological environment of the protein) or in vitro (i.e.,under laboratory conditions). Biological activities of PUFA PKS systemsand the individual proteins/domains that make up a PUFA PKS system havebeen described in detail elsewhere herein. Modifications of a protein,such as in a homologue or mimetic (discussed below), may result inproteins having the same biological activity as the naturally occurringprotein, or in proteins having decreased or increased biologicalactivity as compared to the naturally occurring protein. Modificationswhich result in a decrease in protein expression or a decrease in theactivity of the protein, can be referred to as inactivation (complete orpartial), down-regulation, or decreased action (or activity) of aprotein. Similarly, modifications which result in an increase in proteinexpression or an increase in the activity of the protein, can bereferred to as amplification, overproduction, activation, enhancement,up-regulation or increased action (or activity) of a protein. It isnoted that general reference to a homologue having the biologicalactivity of the wild-type protein does not necessarily mean that thehomologue has identical biological activity as the wild-type protein,particularly with regard to the level of biological activity. Rather, ahomologue can perform the same biological activity as the wild-typeprotein, but at a reduced or increased level of activity as compared tothe wild-type protein. A functional domain of a PUFA PKS system is adomain (i.e., a domain can be a portion of a protein) that is capable ofperforming a biological function (i.e., has biological activity).

Methods of detecting and measuring PUFA PKS protein or domain biologicalactivity include, but are not limited to, measurement of transcriptionof a PUFA PKS protein or domain, measurement of translation of a PUFAPKS protein or domain, measurement of posttranslational modification ofa PUFA PKS protein or domain, measurement of enzymatic activity of aPUFA PKS protein or domain, and/or measurement production of one or moreproducts of a PUFA PKS system (e.g., PUFA production). It is noted thatan isolated protein of the present invention (including a homologue) isnot necessarily required to have the biological activity of thewild-type protein. For example, a PUFA PKS protein or domain can be atruncated, mutated or inactive protein, for example. Such proteins areuseful in screening assays, for example, or for other purposes such asantibody production. In a preferred embodiment, the isolated proteins ofthe present invention have biological activity that is similar to thatof the wild-type protein (although not necessarily equivalent, asdiscussed above).

Methods to measure protein expression levels generally include, but arenot limited to: Western blot, immunoblot, enzyme-linked immunosorbantassay (ELISA), radioimmunoassay (RIA), immunoprecipitation, surfaceplasmon resonance, chemiluminescence, fluorescent polarization,phosphorescence, immunohistochemical analysis, matrix-assisted laserdesorption/ionization time-of-flight (MALDI-TOF) mass spectrometry,microcytometry, microarray, microscopy, fluorescence activated cellsorting (FACS), and flow cytometry, as well as assays based on aproperty of the protein including but not limited to enzymatic activityor interaction with other protein partners. Binding assays are also wellknown in the art. For example, a BIAcore machine can be used todetermine the binding constant of a complex between two proteins. Thedissociation constant for the complex can be determined by monitoringchanges in the refractive index with respect to time as buffer is passedover the chip (O'Shannessy et al. Anal. Biochem. 212:457-468 (1993);Schuster et al., Nature 365:343-347 (1993)). Other suitable assays formeasuring the binding of one protein to another include, for example,immunoassays such as enzyme linked immunoabsorbent assays (ELISA) andradioimmunoassays (RIA); or determination of binding by monitoring thechange in the spectroscopic or optical properties of the proteinsthrough fluorescence, UV absorption, circular dichrosim, or nuclearmagnetic resonance (NMR).

In one embodiment, the present invention relates to an isolated proteincomprising an amino acid sequence selected from the group consisting of:(a) an amino acid sequence selected from the group consisting of: SEQ IDNO:39, SEQ ID NO:52, SEQ ID NO:62, and biologically active fragmentsthereof; (b) an amino acid sequence selected from the group consistingof: SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:48, SEQ IDNO:50, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ IDNO:64, SEQ ID NO:66, SEQ ID NO:68 and biologically active fragmentsthereof; (c) an amino acid sequence that is at least about 60% identicalto at least 500 consecutive amino acids of the amino acid sequence of(a), wherein the amino acid sequence has a biological activity of atleast one domain of a polyunsaturated fatty acid (PUFA) polyketidesynthase (PKS) system; and/or (d) an amino acid sequence that is atleast about 60% identical to the amino acid sequence of (b), wherein theamino acid sequence has a biological activity of at least one domain ofa polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system. Ina further embodiment, an amino acid sequence including the active sitedomains or other functional motifs described above for several of thePUFA PKS domains are encompassed by the invention. In one embodiment,the amino acid sequence described above does not include any of thefollowing amino acid sequences: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6,SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:13, SEQ ID NO:18, SEQ ID NO:20, SEQID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ IDNO:32.

In one aspect of the invention, a PUFA PKS protein or domain encompassedby the present invention, including a homologue of a particular PUFA PKSprotein or domain described herein, comprises an amino acid sequencethat is at least about 60% identical to at least 500 consecutive aminoacids of an amino acid sequence chosen from: SEQ ID NO:39, SEQ ID NO:52,or SEQ ID NO:62, wherein the amino acid sequence has a biologicalactivity of at least one domain of a PUFA PKS system. In a furtheraspect, the amino acid sequence of the protein is at least about 60%identical to at least about 600 consecutive amino acids, and morepreferably to at least about 700 consecutive amino acids, and morepreferably to at least about 800 consecutive amino acids, and morepreferably to at least about 900 consecutive amino acids, and morepreferably to at least about 1000 consecutive amino acids, and morepreferably to at least about 1100 consecutive amino acids, and morepreferably to at least about 1200 consecutive amino acids, and morepreferably to at least about 1300 consecutive amino acids, and morepreferably to at least about 1400 consecutive amino acids of any of SEQID NO:39, SEQ ID NO:52, or SEQ ID NO:62, or to the full length of SEQ IDNO:62. In a further aspect, the amino acid sequence of the protein is atleast about 60% identical to at least about 1500 consecutive aminoacids, and more preferably to at least about 1600 consecutive aminoacids, and more preferably to at least about 1700 consecutive aminoacids, and more preferably to at least about 1800 consecutive aminoacids, and more preferably to at least about 1900 consecutive aminoacids, of any of SEQ ID NO:39 or SEQ ID NO:52, or to the full length ofSEQ ID NO:52. In a further aspect, the amino acid sequence of theprotein is at least about 60% identical to at least about 2000consecutive amino acids, and more preferably to at least about 2100consecutive amino acids, and more preferably to at least about 2200consecutive amino acids, and more preferably to at least about 2300consecutive amino acids, and more preferably to at least about 2400consecutive amino acids, and more preferably to at least about 2500consecutive amino acids, and more preferably to at least about 2600consecutive amino acids, and more preferably to at least about 2700consecutive amino acids, and more preferably to at least about 2800consecutive amino acids, and even more preferably, to the full length ofSEQ ID NO:39. In one embodiment, the amino acid sequence described abovedoes not include any of the following amino acid sequences: SEQ ID NO:2,SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:13, SEQID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ IDNO:28, SEQ ID NO:30, SEQ ID NO:32.

In another aspect, a PUFA PKS protein or domain encompassed by thepresent invention, including homologues as described above, comprises anamino acid sequence that is at least about 65% identical, and morepreferably at least about 70% identical, and more preferably at leastabout 75% identical, and more preferably at least about 80% identical,and more preferably at least about 85% identical, and more preferably atleast about 90% identical, and more preferably at least about 95%identical, and more preferably at least about 96% identical, and morepreferably at least about 97% identical, and more preferably at leastabout 98% identical, and more preferably at least about 99% identical toan amino acid sequence chosen from: SEQ ID NO:39, SEQ ID NO:52, or SEQID NO:62, over any of the consecutive amino acid lengths described inthe paragraph above, wherein the amino acid sequence has a biologicalactivity of at least one domain of a PUFA PKS system. In one embodiment,the amino acid sequence described above does not include any of thefollowing amino acid sequences: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6,SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:13, SEQ ID NO:18, SEQ ID NO:20, SEQID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ IDNO:32.

In one aspect of the invention, a PUFA PKS protein or domain encompassedby the present invention, including a homologue as described above,comprises an amino acid sequence that is at least about 60% identical toan amino acid sequence chosen from: SEQ ID NO:39, SEQ ID NO:41, SEQ IDNO:43, SEQ ID NO:45, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ IDNO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ IDNO:64, SEQ ID NO:66, SEQ ID NO:68, wherein the amino acid sequence has abiological activity of at least one domain of a PUFA PKS system. In afurther aspect, the amino acid sequence of the protein is at least about65% identical, and more preferably at least about 70% identical, andmore preferably at least about 75% identical, and more preferably atleast about 80% identical, and more preferably at least about 85%identical, and more preferably at least about 90% identical, and morepreferably at least about 95% identical, and more preferably at leastabout 96% identical, and more preferably at least about 97% identical,and more preferably at least about 98% identical, and more preferably atleast about 99% identical to an amino acid sequence chosen from: SEQ IDNO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:48, SEQ IDNO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ IDNO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, whereinthe amino acid sequence has a biological activity of at least one domainof a PUFA PKS system. In one embodiment, the amino acid sequencedescribed above does not include any of the following amino acidsequences: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ IDNO:10, SEQ ID NO:13, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ IDNO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32.

In another aspect, a PUFA PKS protein or domain encompassed by thepresent invention, including a homologue as described above, comprisesan amino acid sequence that is at least about 50% identical to an aminoacid sequence chosen from: SEQ ID NO:39, SEQ ID NO:43, SEQ ID NO:50, SEQID NO:52, and SEQ ID NO:58, wherein the amino acid sequence has abiological activity of at least one domain of a PUFA PKS system. Inanother aspect, the amino acid sequence of the protein is at least about55% identical, and more preferably at least about 60% identical, to anamino acid sequence chosen from: SEQ ID NO:39, SEQ ID NO:43, SEQ IDNO:50, SEQ ID NO:52, SEQ ID NO:56 and SEQ ID NO:58, wherein the aminoacid sequence has a biological activity of at least one domain of a PUFAPKS system. In a further aspect, the amino acid sequence of the proteinis at least about 65% identical to an amino acid sequence chosen fromSEQ ID NO:39, SEQ ID NO:43, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54,SEQ ID NO:56 and SEQ ID NO:58, wherein the amino acid sequence has abiological activity of at least one domain of a PUFA PKS system. Inanother aspect, the amino acid sequence of the protein is at least about70% identical, and more preferably at least about 75% identical, to anamino acid sequence chosen from: SEQ ID NO:39, SEQ ID NO:43, SEQ IDNO:45, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ IDNO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, and SEQ ID NO:64,wherein the amino acid sequence has a biological activity of at leastone domain of a PUFA PKS system. In another aspect, the amino acidsequence of the protein is at least about 80% identical, and morepreferably at least about 85% identical, and more preferably at leastabout 90% identical, and more preferably at least about 95% identical,and more preferably at least about 96% identical, and more preferably atleast about 97% identical, and more preferably at least about 98%identical, and more preferably at least about 99% identical, to an aminoacid sequence chosen from: SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQID NO:45, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ IDNO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ IDNO:66, SEQ ID NO:68, wherein the amino acid sequence has a biologicalactivity of at least one domain of a PUFA PKS system. In one embodiment,the amino acid sequence described above does not include any of thefollowing amino acid sequences: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6,SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:13, SEQ ID NO:18, SEQ ID NO:20, SEQID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ IDNO:32.

In a preferred embodiment an isolated protein or domain of the presentinvention comprises, consists essentially of, or consists of, an aminoacid sequence chosen from: SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQID NO:45, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ IDNO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ IDNO:66, SEQ ID NO:68, or any biologically active fragments thereof,including any fragments that have a biological activity of at least onedomain of a PUFA PKS system.

In one aspect of the present invention, the following Schizochytriumproteins and domains are useful in one or more embodiments of thepresent invention, all of which have been previously described in detailin U.S. patent application Ser. No. 10/124,800, supra. In one aspect ofthe invention, a PUFA PKS protein or domain useful in the presentinvention comprises an amino acid sequence that is at least about 60%identical to at least 500 consecutive amino acids of an amino acidsequence chosen from: SEQ ID NO:2, SEQ ID NO:4, and SEQ ID NO:6; whereinthe amino acid sequence has a biological activity of at least one domainof a PUFA PKS system. In a further aspect, the amino acid sequence ofthe protein is at least about 60% identical to at least about 600consecutive amino acids, and more preferably to at least about 700consecutive amino acids, and more preferably to at least about 800consecutive amino acids, and more preferably to at least about 900consecutive amino acids, and more preferably to at least about 1000consecutive amino acids, and more preferably to at least about 1100consecutive amino acids, and more preferably to at least about 1200consecutive amino acids, and more preferably to at least about 1300consecutive amino acids, and more preferably to at least about 1400consecutive amino acids, and more preferably to at least about 1500consecutive amino acids of any of SEQ ID NO:2, SEQ ID NO:4 and SEQ IDNO:6, or to the full length of SEQ ID NO:6. In a further aspect, theamino acid sequence of the protein is at least about 60% identical to atleast about 1600 consecutive amino acids, and more preferably to atleast about 1700 consecutive amino acids, and more preferably to atleast about 1800 consecutive amino acids, and more preferably to atleast about 1900 consecutive amino acids, and more preferably to atleast about 2000 consecutive amino acids of any of SEQ ID NO:2 or SEQ IDNO:4, or to the full length of SEQ ID NO:4. In a further aspect, theamino acid sequence of the protein is at least about 60% identical to atleast about 2100 consecutive amino acids, and more preferably to atleast about 2200 consecutive amino acids, and more preferably to atleast about 2300 consecutive amino acids, and more preferably to atleast about 2400 consecutive amino acids, and more preferably to atleast about 2500 consecutive amino acids, and more preferably to atleast about 2600 consecutive amino acids, and more preferably to atleast about 2700 consecutive amino acids, and more preferably to atleast about 2800 consecutive amino acids, and even more preferably, tothe full length of SEQ ID NO:2.

In another aspect, a PUFA PKS protein or domain useful in one or moreembodiments of the present invention comprises an amino acid sequencethat is at least about 65% identical, and more preferably at least about70% identical, and more preferably at least about 75% identical, andmore preferably at least about 80% identical, and more preferably atleast about 85% identical, and more preferably at least about 90%identical, and more preferably at least about 95% identical, and morepreferably at least about 96% identical, and more preferably at leastabout 97% identical, and more preferably at least about 98% identical,and more preferably at least about 99% identical to an amino acidsequence chosen from: SEQ ID NO:2, SEQ ID NO:4, or SEQ ID NO:6, over anyof the consecutive amino acid lengths described in the paragraph above,wherein the amino acid sequence has a biological activity of at leastone domain of a PUFA PKS system.

In another aspect of the invention, a PUFA PKS protein or domain usefulin one or more embodiments of the present invention comprises an aminoacid sequence that is at least about 60% identical to an amino acidsequence chosen from: SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:13, SEQ IDNO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ IDNO:28, SEQ ID NO:30, or SEQ ID NO:32, wherein the amino acid sequencehas a biological activity of at least one domain of a PUFA PKS system.In a further aspect, the amino acid sequence of the protein is at leastabout 65% identical, and more preferably at least about 70% identical,and more preferably at least about 75% identical, and more preferably atleast about 80% identical, and more preferably at least about 85%identical, and more preferably at least about 90% identical, and morepreferably at least about 95% identical, and more preferably at leastabout 96% identical, and more preferably at least about 97% identical,and more preferably at least about 98% identical, and more preferably atleast about 99% identical to an amino acid sequence chosen from: SEQ IDNO:8, SEQ ID NO:10, SEQ ID NO:13, SEQ ID NO:18, SEQ ID NO:20, SEQ IDNO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ IDNO:32, wherein the amino acid sequence has a biological activity of atleast one domain of a PUFA PKS system.

In yet another aspect of the invention, a PUFA PKS protein or domainuseful in one or more embodiments of the present invention comprises,consists essentially of, or consists of, an amino acid sequence chosenfrom: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10,SEQ ID NO:13, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24,SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32 or anybiologically active fragments thereof, including any fragments that havea biological activity of at least one domain of a PUFA PKS system.

According to the present invention, the term “contiguous” or“consecutive”, with regard to nucleic acid or amino acid sequencesdescribed herein, means to be connected in an unbroken sequence. Forexample, for a first sequence to comprise 30 contiguous (or consecutive)amino acids of a second sequence, means that the first sequence includesan unbroken sequence of 30 amino acid residues that is 100% identical toan unbroken sequence of 30 amino acid residues in the second sequence.Similarly, for a first sequence to have “100% identity” with a secondsequence means that the first sequence exactly matches the secondsequence with no gaps between nucleotides or amino acids.

As used herein, unless otherwise specified, reference to a percent (%)identity refers to an evaluation of homology which is performed using:(1) a BLAST 2.0 Basic BLAST homology search using blastp for amino acidsearches, blastn for nucleic acid searches, and blastX for nucleic acidsearches and searches of translated amino acids in all 6 open readingframes, all with standard default parameters, wherein the query sequenceis filtered for low complexity regions by default (described inAltschul, S. F., Madden, T. L., Schääffer, A. A., Zhang, J., Zhang, Z.,Miller, W. & Lipman, D. J. (1997) “Gapped BLAST and PSI-BLAST: a newgeneration of protein database search programs.” Nucleic Acids Res.25:3389-3402, incorporated herein by reference in its entirety); (2) aBLAST 2 alignment (using the parameters described below); (3) and/orPSI-BLAST with the standard default parameters (Position-SpecificIterated BLAST). It is noted that due to some differences in thestandard parameters between BLAST 2.0 Basic BLAST and BLAST 2, twospecific sequences might be recognized as having significant homologyusing the BLAST 2 program, whereas a search performed in BLAST 2.0 BasicBLAST using one of the sequences as the query sequence may not identifythe second sequence in the top matches. In addition, PSI-BLAST providesan automated, easy-to-use version of a “profile” search, which is asensitive way to look for sequence homologues. The program firstperforms a gapped BLAST database search. The PSI-BLAST program uses theinformation from any significant alignments returned to construct aposition-specific score matrix, which replaces the query sequence forthe next round of database searching. Therefore, it is to be understoodthat percent identity can be determined by using any one of theseprograms.

Two specific sequences can be aligned to one another using BLAST 2sequence as described in Tatusova and Madden, (1999), “Blast 2sequences—a new tool for comparing protein and nucleotide sequences”,FEMS Microbiol Lett. 174, 247, incorporated herein by reference in itsentirety. BLAST 2 sequence alignment is performed in blastp or blastnusing the BLAST 2.0 algorithm to perform a Gapped BLAST search (BLAST2.0) between the two sequences allowing for the introduction of gaps(deletions and insertions) in the resulting alignment. For purposes ofclarity herein, a BLAST 2 sequence alignment is performed using thestandard default parameters as follows.

For blastn, using 0 BLOSUM62 matrix:

Reward for match=1

Penalty for mismatch=−2

Open gap (5) and extension gap (2) penalties

gap x_dropoff (50) expect (10) word size (11) filter (on)

For blastp, using 0 BLOSUM62 matrix:

Open gap (11) and extension gap (1) penalties

gap x_dropoff (50) expect (10) word size (3) filter (on).

According to the present invention, an amino acid sequence that has abiological activity of at least one domain of a PUFA PKS system is anamino acid sequence that has the biological activity of at least onedomain of the PUFA PKS system described in detail herein, as previouslyexemplified by the Schizochytrium PUFA PKS system or as additionallyexemplified herein by the Thraustochytrium PUFA PKS system. Thebiological activities of the various domains within the Schizochytriumor Thraustochytrium PUFA PKS systems have been described in detailabove. Therefore, an isolated protein useful in the present inventioncan include the translation product of any PUFA PKS open reading frame,any PUFA PKS domain, biologically active fragment thereof, or anyhomologue of a naturally occurring PUFA PKS open reading frame productor domain which has biological activity.

In another embodiment of the invention, an amino acid sequence havingthe biological activity of at least one domain of a PUFA PKS system ofthe present invention includes an amino acid sequence that issufficiently similar to a naturally occurring PUFA PKS protein orpolypeptide that a nucleic acid sequence encoding the amino acidsequence is capable of hybridizing under moderate, high, or very highstringency conditions (described below) to (i.e., with) a nucleic acidmolecule encoding the naturally occurring PUFA PKS protein orpolypeptide (i.e., to the complement of the nucleic acid strand encodingthe naturally occurring PUFA PKS protein or polypeptide). Preferably, anamino acid sequence having the biological activity of at least onedomain of a PUFA PKS system of the present invention is encoded by anucleic acid sequence that hybridizes under moderate, high or very highstringency conditions to the complement of a nucleic acid sequence thatencodes any of the above-described amino acid sequences for a PUFA PKSprotein or domain. Methods to deduce a complementary sequence are knownto those skilled in the art. It should be noted that since amino acidsequencing and nucleic acid sequencing technologies are not entirelyerror-free, the sequences presented herein, at best, represent apparentsequences of PUFA PKS domains and proteins of the present invention.

As used herein, hybridization conditions refer to standard hybridizationconditions under which nucleic acid molecules are used to identifysimilar nucleic acid molecules. Such standard conditions are disclosed,for example, in Sambrook et al., Molecular Cloning: A Laboratory Manual,Cold Spring Harbor Labs Press, 1989. Sambrook et al., ibid., isincorporated by reference herein in its entirety (see specifically,pages 9.31-9.62). In addition, formulae to calculate the appropriatehybridization and wash conditions to achieve hybridization permittingvarying degrees of mismatch of nucleotides are disclosed, for example,in Meinkoth et al., 1984, Anal. Biochem. 138, 267-284; Meinkoth et al.,ibid., is incorporated by reference herein in its entirety.

More particularly, moderate stringency hybridization and washingconditions, as referred to herein, refer to conditions which permitisolation of nucleic acid molecules having at least about 70% nucleicacid sequence identity with the nucleic acid molecule being used toprobe in the hybridization reaction (i.e., conditions permitting about30% or less mismatch of nucleotides). High stringency hybridization andwashing conditions, as referred to herein, refer to conditions whichpermit isolation of nucleic acid molecules having at least about 80%nucleic acid sequence identity with the nucleic acid molecule being usedto probe in the hybridization reaction (i.e., conditions permittingabout 20% or less mismatch of nucleotides). Very high stringencyhybridization and washing conditions, as referred to herein, refer toconditions which permit isolation of nucleic acid molecules having atleast about 90% nucleic acid sequence identity with the nucleic acidmolecule being used to probe in the hybridization reaction (i.e.,conditions permitting about 10% or less mismatch of nucleotides). Asdiscussed above, one of skill in the art can use the formulae inMeinkoth et al., ibid. to calculate the appropriate hybridization andwash conditions to achieve these particular levels of nucleotidemismatch. Such conditions will vary, depending on whether DNA:RNA orDNA:DNA hybrids are being formed. Calculated melting temperatures forDNA:DNA hybrids are 10° C. less than for DNA:RNA hybrids. In particularembodiments, stringent hybridization conditions for DNA:DNA hybridsinclude hybridization at an ionic strength of 6×SSC (0.9 M Na⁺) at atemperature of between about 20° C. and about 35° C. (lower stringency),more preferably, between about 28° C. and about 40° C. (more stringent),and even more preferably, between about 35° C. and about 45° C. (evenmore stringent), with appropriate wash conditions. In particularembodiments, stringent hybridization conditions for DNA:RNA hybridsinclude hybridization at an ionic strength of 6×SSC (0.9 M Na⁺) at atemperature of between about 30° C. and about 45° C., more preferably,between about 38° C. and about 50° C., and even more preferably, betweenabout 45° C. and about 55° C., with similarly stringent wash conditions.These values are based on calculations of a melting temperature formolecules larger than about 100 nucleotides, 0% formamide and a G+Ccontent of about 40%. Alternatively, T_(m) can be calculated empiricallyas set forth in Sambrook et al., supra, pages 9.31 to 9.62. In general,the wash conditions should be as stringent as possible, and should beappropriate for the chosen hybridization conditions. For example,hybridization conditions can include a combination of salt andtemperature conditions that are approximately 20-25° C. below thecalculated T_(m) of a particular hybrid, and wash conditions typicallyinclude a combination of salt and temperature conditions that areapproximately 12-20° C. below the calculated T_(m) of the particularhybrid. One example of hybridization conditions suitable for use withDNA:DNA hybrids includes a 2-24 hour hybridization in 6×SSC (50%formamide) at about 42° C., followed by washing steps that include oneor more washes at room temperature in about 2×SSC, followed byadditional washes at higher temperatures and lower ionic strength (e.g.,at least one wash as about 37° C. in about 0.1×-0.5×SSC, followed by atleast one wash at about 68° C. in about 0.1×-0.5×SSC).

The present invention also includes a fusion protein that includes anyPUFA PKS protein or domain or any homologue or fragment thereof attachedto one or more fusion segments. Suitable fusion segments for use withthe present invention include, but are not limited to, segments thatcan: enhance a protein's stability; provide other desirable biologicalactivity; and/or assist with the purification of the protein (e.g., byaffinity chromatography). A suitable fusion segment can be a domain ofany size that has the desired function (e.g., imparts increasedstability, solubility, biological activity; and/or simplifiespurification of a protein). Fusion segments can be joined to aminoand/or carboxyl termini of the protein and can be susceptible tocleavage in order to enable straight-forward recovery of the desiredprotein. Fusion proteins are preferably produced by culturing arecombinant cell transfected with a fusion nucleic acid molecule thatencodes a protein including the fusion segment attached to either thecarboxyl and/or amino terminal end of the protein of the invention asdiscussed above.

In one embodiment of the present invention, any of the above-describedPUFA PKS amino acid sequences, as well as homologues of such sequences,can be produced with from at least one, and up to about 20, additionalheterologous amino acids flanking each of the C- and/or N-terminal endof the given amino acid sequence. The resulting protein or polypeptidecan be referred to as “consisting essentially of” a given amino acidsequence. According to the present invention, the heterologous aminoacids are a sequence of amino acids that are not naturally found (i.e.,not found in nature, in vivo) flanking the given amino acid sequence orwhich would not be encoded by the nucleotides that flank the naturallyoccurring nucleic acid sequence encoding the given amino acid sequenceas it occurs in the gene, if such nucleotides in the naturally occurringsequence were translated using standard codon usage for the organismfrom which the given amino acid sequence is derived. Similarly, thephrase “consisting essentially of”, when used with reference to anucleic acid sequence herein, refers to a nucleic acid sequence encodinga given amino acid sequence that can be flanked by from at least one,and up to as many as about 60, additional heterologous nucleotides ateach of the 5′ and/or the 3′ end of the nucleic acid sequence encodingthe given amino acid sequence. The heterologous nucleotides are notnaturally found (i.e., not found in nature, in vivo) flanking thenucleic acid sequence encoding the given amino acid sequence as itoccurs in the natural gene.

The minimum size of a protein or domain and/or a homologue or fragmentthereof of the present invention is, in one aspect, a size sufficient tohave the requisite biological activity, or sufficient to serve as anantigen for the generation of an antibody or as a target in an in vitroassay. In one embodiment, a protein of the present invention is at leastabout 8 amino acids in length (e.g., suitable for an antibody epitope oras a detectable peptide in an assay), or at least about 25 amino acidsin length, or at least about 50 amino acids in length, or at least about100 amino acids in length, or at least about 150 amino acids in length,or at least about 200 amino acids in length, or at least about 250 aminoacids in length, or at least about 300 amino acids in length, or atleast about 350 amino acids in length, or at least about 400 amino acidsin length, or at least about 450 amino acids in length, or at leastabout 500 amino acids in length, or at least about 750 amino acids inlength, and so on, in any length between 8 amino acids and up to thefull length of a protein or domain of the invention or longer, in wholeintegers (e.g., 8, 9, 10, . . . 25, 26, . . . 500, 501, . . . 1234,1235, . . . ). There is no limit, other than a practical limit, on themaximum size of such a protein in that the protein can include a portionof a PUFA PKS protein, domain, or biologically active or useful fragmentthereof, or a full-length PUFA PKS protein or domain, plus additionalsequence (e.g., a fusion protein sequence), if desired.

Further embodiments of the present invention include isolated nucleicacid molecules comprising, consisting essentially of, or consisting ofnucleic acid sequences that encode any of the above-identified proteinsor domains, including a homologue or fragment thereof, as well asnucleic acid sequences that are fully complementary thereto. Inaccordance with the present invention, an isolated nucleic acid moleculeis a nucleic acid molecule that has been removed from its natural milieu(i.e., that has been subject to human manipulation), its natural milieubeing the genome or chromosome in which the nucleic acid molecule isfound in nature. As such, “isolated” does not necessarily reflect theextent to which the nucleic acid molecule has been purified, butindicates that the molecule does not include an entire genome or anentire chromosome in which the nucleic acid molecule is found in nature.An isolated nucleic acid molecule can include a gene. An isolatednucleic acid molecule that includes a gene is not a fragment of achromosome that includes such gene, but rather includes the codingregion and regulatory regions associated with the gene, but noadditional genes naturally found on the same chromosome. An isolatednucleic acid molecule can also include a specified nucleic acid sequenceflanked by (i.e., at the 5′ and/or the 3′ end of the sequence)additional nucleic acids that do not normally flank the specifiednucleic acid sequence in nature (i.e., heterologous sequences). Isolatednucleic acid molecule can include DNA, RNA (e.g., mRNA), or derivativesof either DNA or RNA (e.g., cDNA). Although the phrase “nucleic acidmolecule” primarily refers to the physical nucleic acid molecule and thephrase “nucleic acid sequence” primarily refers to the sequence ofnucleotides on the nucleic acid molecule, the two phrases can be usedinterchangeably, especially with respect to a nucleic acid molecule, ora nucleic acid sequence, being capable of encoding a protein or domainof a protein.

Preferably, an isolated nucleic acid molecule of the present inventionis produced using recombinant DNA technology (e.g., polymerase chainreaction (PCR) amplification, cloning) or chemical synthesis. Isolatednucleic acid molecules include natural nucleic acid molecules andhomologues thereof, including, but not limited to, natural allelicvariants and modified nucleic acid molecules in which nucleotides havebeen inserted, deleted, substituted, and/or inverted in such a mannerthat such modifications provide the desired effect on PUFA PKS systembiological activity as described herein. Protein homologues (e.g.,proteins encoded by nucleic acid homologues) have been discussed indetail above.

A nucleic acid molecule homologue can be produced using a number ofmethods known to those skilled in the art (see, for example, Sambrook etal., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor LabsPress, 1989). For example, nucleic acid molecules can be modified usinga variety of techniques including, but not limited to, classicmutagenesis techniques and recombinant DNA techniques, such assite-directed mutagenesis, chemical treatment of a nucleic acid moleculeto induce mutations, restriction enzyme cleavage of a nucleic acidfragment, ligation of nucleic acid fragments, PCR amplification and/ormutagenesis of selected regions of a nucleic acid sequence, synthesis ofoligonucleotide mixtures and ligation of mixture groups to “build” amixture of nucleic acid molecules and combinations thereof. Nucleic acidmolecule homologues can be selected from a mixture of modified nucleicacids by screening for the function of the protein encoded by thenucleic acid and/or by hybridization with a wild-type gene.

The minimum size of a nucleic acid molecule of the present invention isa size sufficient to form a probe or oligonucleotide primer that iscapable of forming a stable hybrid (e.g., under moderate, high or veryhigh stringency conditions) with the complementary sequence of a nucleicacid molecule useful in the present invention, or of a size sufficientto encode an amino acid sequence having a biological activity of atleast one domain of a PUFA PKS system according to the presentinvention. As such, the size of the nucleic acid molecule encoding sucha protein can be dependent on nucleic acid composition and percenthomology or identity between the nucleic acid molecule and complementarysequence as well as upon hybridization conditions per se (e.g.,temperature, salt concentration, and formamide concentration). Theminimal size of a nucleic acid molecule that is used as anoligonucleotide primer or as a probe is typically at least about 12 toabout 15 nucleotides in length if the nucleic acid molecules are GC-richand at least about 15 to about 18 bases in length if they are AT-rich.There is no limit, other than a practical limit, on the maximal size ofa nucleic acid molecule of the present invention, in that the nucleicacid molecule can include a sequence sufficient to encode a biologicallyactive fragment of a domain of a PUFA PKS system, an entire domain of aPUFA PKS system, several domains within an open reading frame (Orf) of aPUFA PKS system, an entire Orf of a PUFA PKS system, or more than oneOrf of a PUFA PKS system.

In one embodiment of the present invention, an isolated nucleic acidmolecule comprises, consists essentially of, or consists of a nucleicacid sequence encoding any of the above-described amino acid sequences,including any of the amino acid sequences, or homologues thereof, from aSchizochytrium or Thraustochytrium described herein. In one aspect, thenucleic acid sequence is selected from the group of: SEQ ID NO:1, SEQ IDNO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:12, SEQ ID NO:17,SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27,SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42,SEQ ID NO:44, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53,SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63,SEQ ID NO:65, or SEQ ID NO:67, or homologues (including sequences thatare at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%,96%, 97%, 98%, or 99% identical to such sequences), or fragmentsthereof, or any complementary sequences thereof.

Another embodiment of the present invention includes a recombinantnucleic acid molecule comprising a recombinant vector and a nucleic acidsequence encoding protein or peptide having a biological activity of atleast one domain (or homologue or fragment thereof) of a PUFA PKS systemas described herein. Such nucleic acid sequences are described in detailabove. According to the present invention, a recombinant vector is anengineered (i.e., artificially produced) nucleic acid molecule that isused as a tool for manipulating a nucleic acid sequence of choice andfor introducing such a nucleic acid sequence into a host cell. Therecombinant vector is therefore suitable for use in cloning, sequencing,and/or otherwise manipulating the nucleic acid sequence of choice, suchas by expressing and/or delivering the nucleic acid sequence of choiceinto a host cell to form a recombinant cell. Such a vector typicallycontains heterologous nucleic acid sequences, that is nucleic acidsequences that are not naturally found adjacent to nucleic acid sequenceto be cloned or delivered, although the vector can also containregulatory nucleic acid sequences (e.g., promoters, untranslatedregions) which are naturally found adjacent to nucleic acid molecules ofthe present invention or which are useful for expression of the nucleicacid molecules of the present invention (discussed in detail below). Thevector can be either RNA or DNA, either prokaryotic or eukaryotic, andtypically is a plasmid. The vector can be maintained as anextrachromosomal element (e.g., a plasmid) or it can be integrated intothe chromosome of a recombinant organism (e.g., a microbe or a plant).The entire vector can remain in place within a host cell, or undercertain conditions, the plasmid DNA can be deleted, leaving behind thenucleic acid molecule of the present invention. The integrated nucleicacid molecule can be under chromosomal promoter control, under native orplasmid promoter control, or under a combination of several promotercontrols. Single or multiple copies of the nucleic acid molecule can beintegrated into the chromosome. A recombinant vector of the presentinvention can contain at least one selectable marker.

In one embodiment, a recombinant vector used in a recombinant nucleicacid molecule of the present invention is an expression vector. As usedherein, the phrase “expression vector” is used to refer to a vector thatis suitable for production of an encoded product (e.g., a protein ofinterest). In this embodiment, a nucleic acid sequence encoding theproduct to be produced (e.g., a PUFA PKS domain) is inserted into therecombinant vector to produce a recombinant nucleic acid molecule. Thenucleic acid sequence encoding the protein to be produced is insertedinto the vector in a manner that operatively links the nucleic acidsequence to regulatory sequences in the vector which enable thetranscription and translation of the nucleic acid sequence within therecombinant host cell.

In another embodiment, a recombinant vector used in a recombinantnucleic acid molecule of the present invention is a targeting vector. Asused herein, the phrase “targeting vector” is used to refer to a vectorthat is used to deliver a particular nucleic acid molecule into arecombinant host cell, wherein the nucleic acid molecule is used todelete or inactivate an endogenous gene within the host cell ormicroorganism (i.e., used for targeted gene disruption or knock-outtechnology). Such a vector may also be known in the art as a “knock-out”vector. In one aspect of this embodiment, a portion of the vector, butmore typically, the nucleic acid molecule inserted into the vector(i.e., the insert), has a nucleic acid sequence that is homologous to anucleic acid sequence of a target gene in the host cell (i.e., a genewhich is targeted to be deleted or inactivated). The nucleic acidsequence of the vector insert is designed to bind to the target genesuch that the target gene and the insert undergo homologousrecombination, whereby the endogenous target gene is deleted,inactivated or attenuated (i.e., by at least a portion of the endogenoustarget gene being mutated or deleted). The use of this type ofrecombinant vector to replace an endogenous Schizochytrium gene with arecombinant gene is described in the Examples section, and the generaltechnique for genetic transformation of Thraustochytrids is described indetail in U.S. patent application Ser. No. 10/124,807, published as U.S.Patent Application Publication No. 20030166207, published Sep. 4, 2003.

Typically, a recombinant nucleic acid molecule includes at least onenucleic acid molecule of the present invention operatively linked to oneor more expression control sequences. As used herein, the phrase“recombinant molecule” or “recombinant nucleic acid molecule” primarilyrefers to a nucleic acid molecule or nucleic acid sequence operativelylinked to a expression control sequence, but can be used interchangeablywith the phrase “nucleic acid molecule”, when such nucleic acid moleculeis a recombinant molecule as discussed herein. According to the presentinvention, the phrase “operatively linked” refers to linking a nucleicacid molecule to an expression control sequence (e.g., a transcriptioncontrol sequence and/or a translation control sequence) in a manner suchthat the molecule is able to be expressed when transfected (i.e.,transformed, transduced, transfected, conjugated or conduced) into ahost cell. Transcription control sequences are sequences which controlthe initiation, elongation, or termination of transcription.Particularly important transcription control sequences are those whichcontrol transcription initiation, such as promoter, enhancer, operatorand repressor sequences. Suitable transcription control sequencesinclude any transcription control sequence that can function in a hostcell or organism into which the recombinant nucleic acid molecule is tobe introduced.

Recombinant nucleic acid molecules of the present invention can alsocontain additional regulatory sequences, such as translation regulatorysequences, origins of replication, and other regulatory sequences thatare compatible with the recombinant cell. In one embodiment, arecombinant molecule of the present invention, including those which areintegrated into the host cell chromosome, also contains secretorysignals (i.e., signal segment nucleic acid sequences) to enable anexpressed protein to be secreted from the cell that produces theprotein. Suitable signal segments include a signal segment that isnaturally associated with the protein to be expressed or anyheterologous signal segment capable of directing the secretion of theprotein according to the present invention. In another embodiment, arecombinant molecule of the present invention comprises a leadersequence to enable an expressed protein to be delivered to and insertedinto the membrane of a host cell. Suitable leader sequences include aleader sequence that is naturally associated with the protein, or anyheterologous leader sequence capable of directing the delivery andinsertion of the protein to the membrane of a cell.

The present inventors have found that the Schizochytrium PUFA PKS Orfs Aand B are closely linked in the genome and region between the Orfs hasbeen sequenced. The Orfs are oriented in opposite directions and 4244base pairs separate the start (ATG) codons (i.e. they are arranged asfollows: 3′OrfA5′-4244 bp-5′OrfB3′). Examination of the 4244 bpintergenic region did not reveal any obvious Orfs (no significantmatches were found on a BlastX search). Both Orfs A and B are highlyexpressed in Schizochytrium, at least during the time of oil production,implying that active promoter elements are embedded in this intergenicregion. These genetic elements are believed to have utility as abi-directional promoter sequence for transgenic applications. Forexample, in a preferred embodiment, one could clone this region, placeany genes of interest at each end and introduce the construct intoSchizochytrium (or some other host in which the promoters can be shownto function). It is predicted that the regulatory elements, under theappropriate conditions, would provide for coordinated, high levelexpression of the two introduced genes. The complete nucleotide sequencefor the regulatory region containing Schizochytrium PUFA PKS regulatoryelements (e.g., a promoter) is represented herein as SEQ ID NO:36.

In a similar manner, OrfC is highly expressed in Schizochytrium duringthe time of oil production and regulatory elements are expected toreside in the region upstream of its start codon. A region of genomicDNA upstream of OrfC has been cloned and sequenced and is representedherein as (SEQ ID NO:37). This sequence contains the 3886 nt immediatelyupstream of the OrfC start codon. Examination of this region did notreveal any obvious Orfs (i.e., no significant matches were found on aBlastX search). It is believed that regulatory elements contained inthis region, under the appropriate conditions, will provide forhigh-level expression of a gene placed behind them. Additionally, underthe appropriate conditions, the level of expression may be coordinatedwith genes under control of the A-B intergenic region (SEQ ID NO:36).

Therefore, in one embodiment, a recombinant nucleic acid molecule usefulin the present invention, as disclosed herein, can include a PUFA PKSregulatory region contained within SEQ ID NO:36 and/or SEQ ID NO:37.Such a regulatory region can include any portion (fragment) of SEQ IDNO:36 and/or SEQ ID NO:37 that has at least basal PUFA PKStranscriptional activity.

One or more recombinant molecules of the present invention can be usedto produce an encoded product (e.g., a PUFA PKS domain, protein, orsystem) of the present invention. In one embodiment, an encoded productis produced by expressing a nucleic acid molecule as described hereinunder conditions effective to produce the protein. A preferred method toproduce an encoded protein is by transfecting a host cell with one ormore recombinant molecules to form a recombinant cell. Suitable hostcells to transfect include, but are not limited to, any bacterial,fungal (e.g., yeast), insect, plant or animal cell that can betransfected. In one embodiment of the invention, a preferred host cellis a Thraustochytrid host cell (described in detail below) or a planthost cell. Host cells can be either untransfected cells or cells thatare already transfected with at least one other recombinant nucleic acidmolecule.

According to the present invention, the term “transfection” is used torefer to any method by which an exogenous nucleic acid molecule (i.e., arecombinant nucleic acid molecule) can be inserted into a cell. The term“transformation” can be used interchangeably with the term“transfection” when such term is used to refer to the introduction ofnucleic acid molecules into microbial cells, such as algae, bacteria andyeast, or into plants. In microbial systems, the term “transformation”is used to describe an inherited change due to the acquisition ofexogenous nucleic acids by the microorganism or plant and is essentiallysynonymous with the term “transfection.” However, in animal cells,transformation has acquired a second meaning which can refer to changesin the growth properties of cells in culture after they becomecancerous, for example. Therefore, to avoid confusion, the term“transfection” is preferably used with regard to the introduction ofexogenous nucleic acids into animal cells, and the term “transfection”will be used herein to generally encompass transfection of animal cells,and transformation of microbial cells or plant cells, to the extent thatthe terms pertain to the introduction of exogenous nucleic acids into acell. Therefore, transfection techniques include, but are not limitedto, transformation, particle bombardment, diffusion, active transport,bath sonication, electroporation, microinjection, lipofection,adsorption, infection and protoplast fusion.

It will be appreciated by one skilled in the art that use of recombinantDNA technologies can improve control of expression of transfectednucleic acid molecules by manipulating, for example, the number ofcopies of the nucleic acid molecules within the host cell, theefficiency with which those nucleic acid molecules are transcribed, theefficiency with which the resultant transcripts are translated, and theefficiency of post-translational modifications. Additionally, thepromoter sequence might be genetically engineered to improve the levelof expression as compared to the native promoter. Recombinant techniquesuseful for controlling the expression of nucleic acid molecules include,but are not limited to, integration of the nucleic acid molecules intoone or more host cell chromosomes, addition of vector stabilitysequences to plasmids, substitutions or modifications of transcriptioncontrol signals (e.g., promoters, operators, enhancers), substitutionsor modifications of translational control signals (e.g., ribosomebinding sites, Shine-Dalgarno sequences), modification of nucleic acidmolecules to correspond to the codon usage of the host cell, anddeletion of sequences that destabilize transcripts.

General discussion above with regard to recombinant nucleic acidmolecules and transfection of host cells is intended to be applied toany recombinant nucleic acid molecule discussed herein, including thoseencoding any amino acid sequence having a biological activity of atleast one domain from a PUFA PKS, those encoding amino acid sequencesfrom other PKS systems, and those encoding other proteins or domains.

Polyunsaturated fatty acids (PUFAs) are essential membrane components inhigher eukaryotes and the precursors of many lipid-derived signalingmolecules. The PUFA PKS system of the present invention uses pathwaysfor PUFA synthesis that do not require desaturation and elongation ofsaturated fatty acids. The pathways catalyzed by PUFA PKSs that aredistinct from previously recognized PKSs in both structure andmechanism. Generation of cis double bonds is suggested to involveposition-specific isomerases; these enzymes are believed to be useful inthe production of new families of antibiotics.

To produce significantly high yields of one or more desiredpolyunsaturated fatty acids or other bioactive molecules, an organism,preferably a microorganism or a plant, and most preferably aThraustochytrid microorganism, can be genetically modified to alter theactivity and particularly, the end product, of the PUFA PKS system inthe microorganism or plant.

Therefore, one embodiment of the present invention relates to agenetically modified microorganism, wherein the microorganism expressesa PKS system comprising at least one biologically active domain of apolyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system. Thedomain of the PUFA PKS system can include any of the domains, includinghomologues thereof, for PUFA PKS systems as described above (e.g., forSchizochytrium and Thraustochytrium), and can also include any domain ofa PUFA PKS system from any other non-bacterial microorganism, includingany eukaryotic microorganism, including any Thraustochytridmicroorganism or any domain of a PUFA PKS system from a microorganismidentified by a screening method as described in U.S. patent applicationSer. No. 10/124,800, supra. The genetic modification affects theactivity of the PKS system in the organism. The screening processdescribed in U.S. patent application Ser. No. 10/124,800 includes thesteps of: (a) selecting a microorganism that produces at least one PUFA;and, (b) identifying a microorganism from (a) that has an ability toproduce increased PUFAs under dissolved oxygen conditions of less thanabout 5% of saturation in the fermentation medium, as compared toproduction of PUFAs by the microorganism under dissolved oxygenconditions of greater than about 5% of saturation, and preferably about10%, and more preferably about 15%, and more preferably about 20% ofsaturation in the fermentation medium.

In one aspect, such an organism can endogenously contain and express aPUFA PKS system, and the genetic modification can be a geneticmodification of one or more of the functional domains of the endogenousPUFA PKS system, whereby the modification has some effect on theactivity of the PUFA PKS system. In another aspect, such an organism canendogenously contain and express a PUFA PKS system, and the geneticmodification can be an introduction of at least one exogenous nucleicacid sequence (e.g., a recombinant nucleic acid molecule), wherein theexogenous nucleic acid sequence encodes at least one biologically activedomain or protein from a second PKS system and/or a protein that affectsthe activity of the PUFA PKS system (e.g., a phosphopantetheinyltransferases (PPTase), discussed below). In yet another aspect, theorganism does not necessarily endogenously (naturally) contain a PUFAPKS system, but is genetically modified to introduce at least onerecombinant nucleic acid molecule encoding an amino acid sequence havingthe biological activity of at least one domain of a PUFA PKS system. Inthis aspect, PUFA PKS activity is affected by introducing or increasingPUFA PKS activity in the organism. Various embodiments associated witheach of these aspects will be discussed in greater detail below.

It is to be understood that a genetic modification of a PUFA PKS systemor an organism comprising a PUFA PKS system can involve the modificationof at least one domain of a PUFA PKS system (including a portion of adomain), more than one or several domains of a PUFA PKS system(including adjacent domains, non-contiguous domains, or domains ondifferent proteins in the PUFA PKS system), entire proteins of the PUFAPKS system, and the entire PUFA PKS system (e.g., all of the proteinsencoded by the PUFA PKS genes). As such, modifications can include asmall modification to a single domain of an endogenous PUFA PKS system;to substitution, deletion or addition to one or more domains or proteinsof a given PUFA PKS system; up to replacement of the entire PUFA PKSsystem in an organism with the PUFA PKS system from a differentorganism. One of skill in the art will understand that any geneticmodification to a PUFA PKS system is encompassed by the invention.

As used herein, a genetically modified microorganism can include agenetically modified bacterium, protist, microalgae, fungus, or othermicrobe, and particularly, any of the genera of the orderThraustochytriales (e.g., a Thraustochytrid) described herein (e.g.,Schizochytrium, Thraustochytrium, Japonochytrium, Labyrinthula,Labyrinthuloides, etc.). Such a genetically modified microorganism has agenome which is modified (i.e., mutated or changed) from its normal(i.e., wild-type or naturally occurring) form such that the desiredresult is achieved (i.e., increased or modified PUFA PKS activity and/orproduction of a desired product using the PKS system). Geneticmodification of a microorganism can be accomplished using classicalstrain development and/or molecular genetic techniques. Such techniquesknown in the art and are generally disclosed for microorganisms, forexample, in Sambrook et al., 1989, Molecular Cloning: A LaboratoryManual, Cold Spring Harbor Labs Press. The reference Sambrook et al.,ibid., is incorporated by reference herein in its entirety. Agenetically modified microorganism can include a microorganism in whichnucleic acid molecules have been inserted, deleted or modified (i.e.,mutated; e.g., by insertion, deletion, substitution, and/or inversion ofnucleotides), in such a manner that such modifications provide thedesired effect within the microorganism.

Preferred microorganism host cells to modify according to the presentinvention include, but are not limited to, any bacteria, protist,microalga, fungus, or protozoa. In one aspect, preferred microorganismsto genetically modify include, but are not limited to, any microorganismof the order Thraustochytriales, including any microorganism in thefamilies Thraustochytriaceae and Labyrinthulaceae. Particularlypreferred host cells for use in the present invention could includemicroorganisms from a genus including, but not limited to:Thraustochytrium, Japonochytrium, Aplanochytrium, Elina andSchizochytrium within the Thraustochytriaceae and Labyrinthula,Labyrinthuloides, and Labyrinthomyxa within the Labyrinthulaceae.Preferred species within these genera include, but are not limited to:any species within Labyrinthula, including Labrinthula sp., Labyrinthulaalgeriensis, Labyrinthula cienkowskii, Labyrinthula chattonii,Labyrinthula coenocystis, Labyrinthula macrocystis, Labyrinthulamacrocystis atlantica, Labyrinthula macrocystis macrocystis,Labyrinthula magnifica, Labyrinthula minuta, Labyrinthula roscoffensis,Labyrinthula valkanovii, Labyrinthula vitellina, Labyrinthula vitellinapacifica, Labyrinthula vitellina vitellina, Labyrinthula zopfii; anyLabyrinthuloides species, including Labyrinthuloides sp.,Labyrinthuloides minuta, Labyrinthuloides schizochytrops; anyLabyrinthomyxa species, including Labyrinthomyxa sp., Labyrinthomyxapohlia, Labyrinthomyxa sauvageaui, any Aplanochytrium species, includingAplanochytrium sp. and Aplanochytrium kerguelensis; any Elina species,including Elina sp., Elina marisalba, Elina sinorifica; anyJapanochytrium species, including Japanochytrium sp., Japanochytriummarinum; any Schizochytrium species, including Schizochytrium sp.,Schizochytrium aggregatum, Schizochytrium limacinum, Schizochytriumminutum, Schizochytrium octosporum; and any Thraustochytrium species,including Thraustochytrium sp., Thraustochytrium aggregatum,Thraustochytrium arudimentale, Thraustochytrium aureum, Thraustochytriumbenthicola, Thraustochytrium globosum, Thraustochytrium kinnei,Thraustochytrium motivum, Thraustochytrium pachydermum, Thraustochytriumproliferum, Thraustochytrium roseum, Thraustochytrium striatum, Ulkeniasp., Ulkenia minuta, Ulkenia profunda, Ulkenia radiate, Ulkeniasarkariana, and Ulkenia visurgensis. Particularly preferred specieswithin these genera include, but are not limited to: any Schizochytriumspecies, including Schizochytrium aggregatum, Schizochytrium limacinum,Schizochytrium minutum; any Thraustochytrium species (including formerUlkenia species such as U. visurgensis, U. amoeboida, U. sarkariana, U.profunda, U. radiata, U. minuta and Ulkenia sp. BP-5601), and includingThraustochytrium striatum, Thraustochytrium aureum, Thraustochytriumroseum; and any Japonochytrium species. Particularly preferred strainsof Thraustochytriales include, but are not limited to: Schizochytriumsp. (S31)(ATCC 20888); Schizochytrium sp. (S8)(ATCC 20889);Schizochytrium sp. (LC-RM)(ATCC 18915); Schizochytrium sp. (SR21);Schizochytrium aggregatum (Goldstein et Belsky)(ATCC 28209);Schizochytrium limacinum (Honda et Yokochi)(IFO 32693); Thraustochytriumsp. (23B)(ATCC 20891); Thraustochytrium striatum (Schneider)(ATCC24473); Thraustochytrium aureum (Goldstein)(ATCC 34304);Thraustochytrium roseum (Goldstein)(ATCC 28210); and Japonochytrium sp.(L1)(ATCC 28207). Other examples of suitable host microorganisms forgenetic modification include, but are not limited to, yeast includingSaccharomyces cerevisiae, Saccharomyces carlsbergensis, or other yeastsuch as Candida, Kluyveromyces, or other fungi, for example, filamentousfungi such as Aspergillus, Neurospora, Penicillium, etc. Bacterial cellsalso may be used as hosts. These include, but are not limited to,Escherichia coli, which can be useful in fermentation processes.Alternatively, and only by way of example, a host such as aLactobacillus species or Bacillus species can be used as a host.

Another embodiment of the present invention relates to a geneticallymodified plant, wherein the plant has been genetically modified torecombinantly express a PKS system comprising at least one biologicallyactive domain of a polyunsaturated fatty acid (PUFA) polyketide synthase(PKS) system. The domain of the PUFA PKS system can include any of thedomains, including homologues thereof, for PUFA PKS systems as describedabove (e.g., for Schizochytrium and/or Thraustochytrium), and can alsoinclude any domain of a PUFA PKS system from any non-bacterialmicroorganism (including any eukaryotic microorganism and any otherThraustochytrid microorganism) or any domain of a PUFA PKS system from amicroorganism identified by a screening method as described in U.S.patent application Ser. No. 10/124,800, supra. The plant can also befurther modified with at least one domain or biologically activefragment thereof of another PKS system, including, but not limited to,bacterial PUFA PKS or PKS systems, Type I PKS systems, Type II PKSsystems, modular PKS systems, and/or any non-bacterial PUFA PKS system(e.g., eukaryotic, Thraustochytrid, Thraustochytriaceae orLabyrinthulaceae, Schizochytrium, etc.).

As used herein, a genetically modified plant can include any geneticallymodified plant including higher plants and particularly, any consumableplants or plants useful for producing a desired bioactive molecule ofthe present invention. Such a genetically modified plant has a genomewhich is modified (i.e., mutated or changed) from its normal (i.e.,wild-type or naturally occurring) form such that the desired result isachieved (i.e., increased or modified PUFA PKS activity and/orproduction of a desired product using the PKS system). Geneticmodification of a plant can be accomplished using classical straindevelopment and/or molecular genetic techniques. Methods for producing atransgenic plant, wherein a recombinant nucleic acid molecule encoding adesired amino acid sequence is incorporated into the genome of theplant, are known in the art. A preferred plant to genetically modifyaccording to the present invention is preferably a plant suitable forconsumption by animals, including humans.

Preferred plants to genetically modify according to the presentinvention (i.e., plant host cells) include, but are not limited to anyhigher plants, and particularly consumable plants, including crop plantsand especially plants used for their oils. Such plants can include, forexample: canola, soybeans, rapeseed, linseed, corn, safflowers,sunflowers and tobacco. Other preferred plants include those plants thatare known to produce compounds used as pharmaceutical agents, flavoringagents, neutraceutical agents, functional food ingredients orcosmetically active agents or plants that are genetically engineered toproduce these compounds/agents.

According to the present invention, a genetically modified microorganismor plant includes a microorganism or plant that has been modified usingrecombinant technology or by classical mutagenesis and screeningtechniques. As used herein, genetic modifications which result in adecrease in gene expression, in the function of the gene, or in thefunction of the gene product (i.e., the protein encoded by the gene) canbe referred to as inactivation (complete or partial), deletion,interruption, blockage or down-regulation of a gene. For example, agenetic modification in a gene which results in a decrease in thefunction of the protein encoded by such gene, can be the result of acomplete deletion of the gene (i.e., the gene does not exist, andtherefore the protein does not exist), a mutation in the gene whichresults in incomplete or no translation of the protein (e.g., theprotein is not expressed), or a mutation in the gene which decreases orabolishes the natural function of the protein (e.g., a protein isexpressed which has decreased or no enzymatic activity or action).Genetic modifications that result in an increase in gene expression orfunction can be referred to as amplification, overproduction,overexpression, activation, enhancement, addition, or up-regulation of agene.

The genetic modification of a microorganism or plant according to thepresent invention preferably affects the activity of the PKS systemexpressed by the microorganism or plant, whether the PKS system isendogenous and genetically modified, endogenous with the introduction ofrecombinant nucleic acid molecules into the organism (with the option ofmodifying the endogenous system or not), or provided completely byrecombinant technology. To alter the PUFA production profile of a PUFAPKS system or organism expressing such system includes causing anydetectable or measurable change in the production of any one or morePUFAs by the host microorganism or plant as compared to in the absenceof the genetic modification (i.e., as compared to the unmodified,wild-type microorganism or plant or the microorganism or plant that isunmodified at least with respect to PUFA synthesis—i.e., the organismmight have other modifications not related to PUFA synthesis). To affectthe activity of a PKS system includes any genetic modification thatcauses any detectable or measurable change or modification in the PKSsystem expressed by the organism as compared to in the absence of thegenetic modification. A detectable change or modification in the PKSsystem can include, but is not limited to: a change or modification(introduction of, increase or decrease) of the expression and/orbiological activity of any one or more of the domains in a modified PUFAPKS system as compared to the endogenous PUFA PKS system in the absenceof genetic modification, the introduction of PKS system activity into anorganism such that the organism now has measurable/detectable PKS systemactivity (i.e., the organism did not contain a PKS system prior to thegenetic modification), the introduction into the organism of afunctional domain from a different PKS system than a PKS systemendogenously expressed by the organism such that the PKS system activityis modified (e.g., a bacterial PUFA PKS domain or a type I PKS domain isintroduced into an organism that endogenously expresses a non-bacterialPUFA PKS system), a change in the amount of a bioactive molecule (e.g.,a PUFA) produced by the PKS system (e.g., the system produces more(increased amount) or less (decreased amount) of a given product ascompared to in the absence of the genetic modification), a change in thetype of a bioactive molecule (e.g., a change in the type of PUFA)produced by the PKS system (e.g., the system produces an additional ordifferent PUFA, a new or different product, or a variant of a PUFA orother product that is naturally produced by the system), and/or a changein the ratio of multiple bioactive molecules produced by the PKS system(e.g., the system produces a different ratio of one PUFA to anotherPUFA, produces a completely different lipid profile as compared to inthe absence of the genetic modification, or places various PUFAs indifferent positions in a triacylglycerol as compared to the naturalconfiguration). Such a genetic modification includes any type of geneticmodification and specifically includes modifications made by recombinanttechnology and by classical mutagenesis.

It should be noted that reference to increasing the activity of afunctional domain or protein in a PUFA PKS system refers to any geneticmodification in the organism containing the domain or protein (or intowhich the domain or protein is to be introduced) which results inincreased functionality of the domain or protein system and can includehigher activity of the domain or protein (e.g., specific activity or invivo enzymatic activity), reduced inhibition or degradation of thedomain or protein system, and overexpression of the domain or protein.For example, gene copy number can be increased, expression levels can beincreased by use of a promoter that gives higher levels of expressionthan that of the native promoter, or a gene can be altered by geneticengineering or classical mutagenesis to increase the activity of thedomain or protein encoded by the gene.

Similarly, reference to decreasing the activity of a functional domainor protein in a PUFA PKS system refers to any genetic modification inthe organism containing such domain or protein (or into which the domainor protein is to be introduced) which results in decreased functionalityof the domain or protein and includes decreased activity of the domainor protein, increased inhibition or degradation of the domain or proteinand a reduction or elimination of expression of the domain or protein.For example, the action of domain or protein of the present inventioncan be decreased by blocking or reducing the production of the domain orprotein, “knocking out” the gene or portion thereof encoding the domainor protein, reducing domain or protein activity, or inhibiting theactivity of the domain or protein. Blocking or reducing the productionof a domain or protein can include placing the gene encoding the domainor protein under the control of a promoter that requires the presence ofan inducing compound in the growth medium. By establishing conditionssuch that the inducer becomes depleted from the medium, the expressionof the gene encoding the domain or protein (and therefore, of proteinsynthesis) could be turned off. The present inventors demonstrate theability to delete (knock out) targeted genes in a Thraustochytridmicroorganism in the Examples section. Blocking or reducing the activityof domain or protein could also include using an excision technologyapproach similar to that described in U.S. Pat. No. 4,743,546,incorporated herein by reference. To use this approach, the geneencoding the protein of interest is cloned between specific geneticsequences that allow specific, controlled excision of the gene from thegenome. Excision could be prompted by, for example, a shift in thecultivation temperature of the culture, as in U.S. Pat. No. 4,743,546,or by some other physical or nutritional signal.

In one embodiment of the present invention, a genetic modificationincludes a modification of a nucleic acid sequence encoding an aminoacid sequence that has a biological activity of at least one domain of anon-bacterial PUFA PKS system as described herein (e.g., a domain, morethan one domain, a protein, or the entire PUFA PKS system, of anendogenous PUFA PKS system of a Thraustochytrid host). Such amodification can be made to an amino acid sequence within anendogenously (naturally) expressed non-bacterial PUFA PKS system,whereby a microorganism that naturally contains such a system isgenetically modified by, for example, classical mutagenesis andselection techniques and/or molecular genetic techniques, includegenetic engineering techniques. Genetic engineering techniques caninclude, for example, using a targeting recombinant vector to delete aportion of an endogenous gene (demonstrated in the Examples), or toreplace a portion of an endogenous gene with a heterologous sequence(demonstrated in the Examples). Examples of heterologous sequences thatcould be introduced into a host genome include sequences encoding atleast one functional domain from another PKS system, such as a differentnon-bacterial PUFA PKS system (e.g., from a eukaryote, including anotherThraustochytrid), a bacterial PUFA PKS system, a type I PKS system, atype II PKS system, or a modular PKS system. A heterologous sequence canalso include an entire PUFA PKS system (e.g., all genes associated withthe PUFA PKS system) that is used to replace the entire endogenous PUFAPKS system (e.g., all genes of the endogenous PUFA PKS system) in ahost. A heterologous sequence can also include a sequence encoding amodified functional domain (a homologue) of a natural domain from a PUFAPKS system of a host Thraustochytrid (e.g., a nucleic acid sequenceencoding a modified domain from OrfB of a Schizochytrium, wherein themodified domain will, when used to replace the naturally occurringdomain expressed in the Schizochytrium, alter the PUFA productionprofile by the Schizochytrium). Other heterologous sequences tointroduce into the genome of a host includes a sequence encoding aprotein or functional domain that is not a domain of a PKS system, butwhich will affect the activity of the endogenous PKS system. Forexample, one could introduce into the host genome a nucleic acidmolecule encoding a phosphopantetheinyl transferase (discussed below).Specific modifications that could be made to an endogenous PUFA PKSsystem are discussed in detail herein.

In another aspect of this embodiment of the invention, the geneticmodification can include: (1) the introduction of a recombinant nucleicacid molecule encoding an amino acid sequence having a biologicalactivity of at least one domain of a PUFA PKS system; and/or (2) theintroduction of a recombinant nucleic acid molecule encoding a proteinor functional domain that affects the activity of a PUFA PKS system,into a host. The host can include: (1) a host cell that does not expressany PKS system, wherein all functional domains of a PKS system areintroduced into the host cell, and wherein at least one functionaldomain is from a non-bacterial PUFA PKS system; (2) a host cell thatexpresses a PKS system (endogenous or recombinant) having at least onefunctional domain of a non-bacterial PUFA PKS system, wherein theintroduced recombinant nucleic acid molecule can encode at least oneadditional non-bacterial PUFA PKS domain function or another protein ordomain that affects the activity of the host PKS system; and (3) a hostcell that expresses a PKS system (endogenous or recombinant) which doesnot necessarily include a domain function from a non-bacterial PUFA PKS,and wherein the introduced recombinant nucleic acid molecule includes anucleic acid sequence encoding at least one functional domain of anon-bacterial PUFA PKS system. In other words, the present inventionintends to encompass any genetically modified organism (e.g.,microorganism or plant), wherein the organism comprises at least onenon-bacterial PUFA PKS domain function (either endogenously orintroduced by recombinant modification), and wherein the geneticmodification has a measurable effect on the non-bacterial PUFA PKSdomain function or on the PKS system when the organism comprises afunctional PKS system.

The present invention encompasses many possible non-bacterial andbacterial microorganisms as either possible host cells for the PUFA PKSsystems described herein and/or as sources for additional geneticmaterial encoding PUFA PKS system proteins and domains for use in thegenetic modifications and methods described herein. For example,microbial organisms with a PUFA PKS system similar to that found inSchizochytrium, such as the Thraustochytrium microorganism discovered bythe present inventors and described in Example 1, can be readilyidentified/isolated/screened by methods to identify other non-bacterialmicroorganisms that have a polyunsaturated fatty acid (PUFA) polyketidesynthase (PKS) system that are described in detail in U.S. PatentApplication Publication No. 20020194641, supra (corresponding to U.S.patent application Ser. No. 10/124,800).

Locations for collection of the preferred types of microbes forscreening for a PUFA PKS system according to the present inventioninclude any of the following: low oxygen environments (or locations nearthese types of low oxygen environments including in the guts of animalsincluding invertebrates that consume microbes or microbe-containingfoods (including types of filter feeding organisms), low or non-oxygencontaining aquatic habitats (including freshwater, saline and marine),and especially at-or near-low oxygen environments (regions) in theoceans. The microbial strains would preferably not be obligate anaerobesbut be adapted to live in both aerobic and low or anoxic environments.Soil environments containing both aerobic and low oxygen or anoxicenvironments would also excellent environments to find these organismsin and especially in these types of soil in aquatic habitats ortemporary aquatic habitats.

A particularly preferred non-bacterial microbial strain to screen foruse as a host and/or a source of PUFA PKS genes according to the presentinvention would be a strain (selected from the group consisting ofalgae, fungi (including yeast), protozoa or protists) that, during aportion of its life cycle, is capable of consuming whole bacterial cells(bacterivory) by mechanisms such as phagocytosis, phagotrophic orendocytic capability and/or has a stage of its life cycle in which itexists as an amoeboid stage or naked protoplast. This method ofnutrition would greatly increase the potential for transfer of abacterial PKS system into a eukaryotic cell if a mistake occurred andthe bacterial cell (or its DNA) did not get digested and instead arefunctionally incorporated into the eukaryotic cell.

Included in the present invention as sources of PUFA PKS genes (andproteins and domains encoded thereby) are any Thraustochytrids otherthan those specifically described herein that contain a PUFA PKS system.Such Thraustochytrids include, but are not limited to, but are notlimited to, any microorganism of the order Thraustochytriales, includingany microorganism in the families Thraustochytriaceae andLabyrinthulaceae, which further comprise a genus including, but notlimited to: Thraustochytrium, Japonochytrium, Aplanochytrium, Elina andSchizochytrium within the Thraustochytriaceae and Labyrinthula,Labyrinthuloides, and Labyrinthomyxa within the Labyrinthulaceae.Preferred species within these genera include, but are not limited to:any species within Labyrinthula, including Labrinthula sp., Labyrinthulaalgeriensis, Labyrinthula cienkowskii, Labyrinthula chattonii,Labyrinthula coenocystis, Labyrinthula macrocystis, Labyrinthulamacrocystis atlantica, Labyrinthula macrocystis macrocystis,Labyrinthula magnifica, Labyrinthula minuta, Labyrinthula roscoffensis,Labyrinthula valkanovii, Labyrinthula vitellina, Labyrinthula vitellinapacifica, Labyrinthula vitellina vitellina, Labyrinthula zopfii; anyLabyrinthuloides species, including Labyrinthuloides sp.,Labyrinthuloides minuta, Labyrinthuloides schizochytrops; anyLabyrinthomyxa species, including Labyrinthomyxa sp., Labyrinthomyxapohlia, Labyrinthomyxa sauvageaui, any Aplanochytrium species, includingAplanochytrium sp. and Aplanochytrium kerguelensis; any Elina species,including Elina sp., Elina marisalba, Elina sinorifica; anyJapanochytrium species, including Japanochytrium sp., Japanochytriummarinum; any Schizochytrium species, including Schizochytrium sp.,Schizochytrium aggregatum, Schizochytrium limacinum, Schizochytriumminutum, Schizochytrium octosporum; and any Thraustochytrium species,including Thraustochytrium sp., Thraustochytrium aggregatum,Thraustochytrium arudimentale, Thraustochytrium aureum, Thraustochytriumbenthicola, Thraustochytrium globosum, Thraustochytrium kinnei,Thraustochytrium motivum, Thraustochytrium pachydermum, Thraustochytriumproliferum, Thraustochytrium roseum, Thraustochytrium striatum, Ulkeniasp., Ulkenia minuta, Ulkenia profunda, Ulkenia radiate, Ulkeniasarkariana, and Ulkenia visurgensis.

It is noted that, without being bound by theory, the present inventorsconsider Labyrinthula and other Labyrinthulaceae as sources of PUFA PKSgenes because the Labyrinthulaceae are closely related to theThraustochytriaceae which are known to possess PUFA PKS genes, theLabyrinthulaceae are known to be bactivorous/phagocytotic, and somemembers of the Labyrinthulaceae have fatty acid/PUFA profiles consistentwith having a PUFA PKS system.

Strains of microbes (other than the members of the Thraustochytrids)capable of bacterivory (especially by phagocytosis or endocytosis) canbe found in the following microbial classes (including but not limitedto example genera):

In the algae and algae-like microbes (including Stramenopiles): of theclass Euglenophyceae (for example genera Euglena, and Peranema), theclass Chrysophyceae (for example the genus Ochromonas), the classDinobryaceae (for example the genera Dinobryon, Platychrysis, andChrysochromulina), the Dinophyceae (including the generaCrypthecodinium, Gymnodinium, Peridinium, Ceratium, Gyrodinium, andOxyrrhis), the class Cryptophyceae (for example the genera Cryptomonas,and Rhodomonas), the class Xanthophyceae (for example the genusOlisthodiscus) (and including forms of algae in which an amoeboid stageoccurs as in the flagellates Rhizochloridaceae, and zoospores/gametes ofAphanochaete pascheri, Bumilleria stigeoclonium and Vaucheria geminata),the class Eustigmatophyceae, and the class Prymnesiopyceae (includingthe genera Prymnesium and Diacronema).

In the Stramenopiles including the: Proteromonads, Opalines,Developayella, Diplophorys, Labyrinthulids, Thraustochytrids,Bicosecids, Oomycetes, Hypochytridiomycetes, Commation, Reticulosphaera,Pelagomonas, Pelapococcus, Ollicola, Aureococcus, Parmales,Raphidiophytes, Synurids, Rhizochromulinaales, Pedinellales,Dictyochales, Chrysomeridales, Sarcinochrysidales, Hydrurales,Hibberdiales, and Chromulinales.

In the Fungi: Class Myxomycetes (form myxamoebae)—slime molds, classAcrasieae including the orders Acrasiceae (for example the genusSappinia), class Guttulinaceae (for example the genera Guttulinopsis,and Guttulina), class Dictysteliaceae (for example the genera Acrasis,Dictyostelium, Polysphondylium, and Coenonia), and class Phycomyceaeincluding the orders Chytridiales, Ancylistales, Blastocladiales,Monoblepharidales, Saprolegniales, Peronosporales, Mucorales, andEntomophthorales.

In the Protozoa: Protozoa strains with life stages capable ofbacterivory (including by phageocytosis) can be selected from the typesclassified as ciliates, flagellates or amoebae. Protozoan ciliatesinclude the groups: Chonotrichs, Colpodids, Cyrtophores, Haptorids,Karyorelicts, Oligohymenophora, Polyhymenophora (spirotrichs), Prostomesand Suctoria. Protozoan flagellates include the Biosoecids, Bodonids,Cercomonads, Chrysophytes (for example the genera Anthophysa,Chrysamoemba, Chrysosphaerella, Dendromonas, Dinobryon, Mallomonas,Ochromonas, Paraphysomonas, Poterioochromonas, Spumella, Syncrypta,Synura, and Uroglena), Collar flagellates, Cryptophytes (for example thegenera Chilomonas, Cryptomonas, Cyanomonas, and Goniomonas),Dinoflagellates, Diplomonads, Euglenoids, Heterolobosea, Pedinellids,Pelobionts, Phalansteriids, Pseudodendromonads, Spongomonads andVolvocales (and other flagellates including the unassigned flagellategenera of Artodiscus, Clautriavia, Helkesimastix, Kathablepharis andMulticilia). Amoeboid protozoans include the groups: Actinophryids,Centrohelids, Desmothoricids, Diplophryids, Eumamoebae, Heterolobosea,Leptomyxids, Nucleariid filose amoebae, Pelebionts, Testate amoebae andVampyrellids (and including the unassigned amoebid genera Gymnophrys,Biomyxa, Microcometes, Reticulomyxa, Belonocystis, Elaeorhanis,Allelogromia, Gromia or Lieberkuhnia). The protozoan orders include thefollowing: Percolomonadeae, Heterolobosea, Lyromonadea, Pseudociliata,Trichomonadea, Hypermastigea, Heteromiteae, Telonemea, Cyathobodonea,Ebridea, Pyytomyxea, Opalinea, Kinetomonadea, Hemimastigea, Protostelea,Myxagastrea, Dictyostelea, Choanomonadea, Apicomonadea, Eogregarinea,Neogregarinea, Coelotrolphea, Eucoccidea, Haemosporea, Piroplasmea,Spirotrichea, Prostomatea, Litostomatea, Phyllopharyngea, Nassophorea,Oligohymenophorea, Colpodea, Karyorelicta, Nucleohelea, Centrohelea,Acantharea, Sticholonchea, Polycystinea, Phaeodarea, Lobosea, Filosea,Athalamea, Monothalamea, Polythalamea, Xenophyophorea, Schizocladea,Holosea, Entamoebea, Myxosporea, Actinomyxea, Halosporea, Paramyxea,Rhombozoa and Orthonectea.

A preferred embodiment of the present invention includes strains of themicroorganisms listed above that have been collected from one of thepreferred habitats listed above.

In some embodiments of this method of the present invention, PUFA PKSsystems from bacteria, including genes and portions thereof (encodingentire PUFA PKS systems, proteins thereof and/or domains thereof) can beused to genetically modify other PUFA PKS systems (e.g., anynon-bacterial PUFA PKS system) and/or microorganisms containing the same(or vice versa) in the embodiments of the invention. In one aspect,novel PUFA PKS systems can be identified in bacteria that are expectedto be particularly useful for creating genetically modifiedmicroorganisms (e.g., genetically modified Thraustochytrids) and/ornovel hybrid constructs encoding PUFA PKS systems for use in the methodsand genetically modified microorganisms and plants of the presentinvention. In one aspect, bacteria that may be particularly useful inthe embodiments of the present invention have PUFA PKS systems, whereinthe PUFA PKS system is capable of producing PUFAs at temperaturesexceeding about 20° C., preferably exceeding about 25° C. and even morepreferably exceeding about 30° C. As described previously herein, themarine bacteria, Shewanella and Vibrio marinus, described in U.S. Pat.No. 6,140,486, do not produce PUFAs at higher temperatures, which limitsthe usefulness of PUFA PKS systems derived from these bacteria,particularly in plant applications under field conditions. Therefore, inone embodiment, the screening method of the present invention can beused to identify bacteria that have a PUFA PKS system, wherein thebacteria are capable of growth and PUFA production at highertemperatures (e.g., above about 15° C., 20° C., 25° C., or 30° C. oreven higher). However, even if the bacteria sources do not grow welland/or produce PUFAs at the higher temperatures, the present inventionencompasses the identification, isolation and use of the PUFA PKSsystems (genes and proteins/domains encoded thereby), wherein the PUFAPKS systems from the bacteria have enzymatic/biological activity attemperatures above about 15° C., 20° C., 25° C., or 30° C. or evenhigher. In one aspect of this embodiment, inhibitors of eukaryoticgrowth such as nystatin (antifungal) or cycloheximide (inhibitor ofeukaryotic protein synthesis) can be added to agar plates used toculture/select initial strains from water samples/soil samples collectedfrom the types of habitats/niches such as marine or estuarian habits, orany other habitat where such bacteria can be found. This process wouldhelp select for enrichment of bacterial strains without (or minimal)contamination of eukaryotic strains. This selection process, incombination with culturing the plates at elevated temperatures (e.g. 30°C.), and then selecting strains that produce at least one PUFA wouldinitially identify candidate bacterial strains with a PUFA PKS systemthat is operative at elevated temperatures (as opposed to thosebacterial strains in the prior art which only exhibit PUFA production attemperatures less than about 20° C. and more preferably below about 5°C.).

However, even in bacteria that do not grow well (or at all) at highertemperatures, or that do not produce at least one PUFA at highertemperatures, such strains can be identified and selected as comprisinga PUFA PKS system by the identification of the ability of the bacteriumto produce PUFAs under any conditions and/or by screening the genome ofthe bacterium for genes that are homologous to other known PUFA PKSgenes from bacteria or non-bacterial organisms (e.g., see Example 7). Toevaluate PUFA PKS function at higher temperatures for genes from anybacterial source, one can produce cell-free extracts and test for PUFAproduction at various temperatures, followed by selection ofmicroorganisms that contain PUFA PKS genes that haveenzymatic/biological activity at higher temperature ranges (e.g., 15°C., 20° C., 25° C., or 30° C. or even higher).

Suitable bacteria to use as hosts for genetic modification include anybacterial strain as discussed above. Particularly suitable bacteria touse as a source of PUFA PKS genes (and proteins and domains encodedthereby) for the production of genetically modified sequences andorganisms according to the present invention include any bacterium thatcomprises a PUFA PKS system. Such bacteria are typically isolated frommarine or estuarian habitats and can be readily identified by theirability to product PUFAs and/or by the presence of one or more geneshaving homology to known PUFA PKS genes in the organism. Such bacteriacan include, but are not limited to, bacteria of the genera Shewanellaand Vibrio. Preferred bacteria for use in the present invention includethose with PUFA PKS systems that are biologically active at highertemperatures (e.g., above about 15° C., 20° C., 25° C., or 30° C. oreven higher). The present inventors have identified two exemplarybacteria (e.g. Shewanella olleyana and Shewanella japonica; see Examples7 and 8) that will be particularly suitable for use as sources of PUFAPKS genes, and others can be readily identified or are known to comprisePUFA PKS genes and may be useful in an embodiment of the presentinvention (e.g., Shewanella gelidimarina).

Furthermore, it is recognized that not all bacterial or non-bacterialmicroorganisms can be readily cultured from natural habitats. However,genetic characteristics of such un-culturable microorganisms can beevaluated by isolating genes from DNA prepared en mass from mixed orcrude environmental samples. Particularly suitable to the presentinvention, PUFA PKS genes derived from un-culturable microorganisms canbe isolated from environmental DNA samples by degenerate PCR usingprimers designed to generally match regions of high similarity in knownPUFA PKS genes (e.g., see Example 7). Alternatively, whole DNA fragmentscan be cloned directly from purified environmental DNA by any of severalmethods known to the art. Sequence of the DNA fragments thus obtainedcan reveal homologs to known genes such as PUFA PKS genes. Homologs ofOrfB and OrfC (referring to the domain structure of Schizochytrium andThraustochytrium, for example) may be particularly useful in definingthe PUFA PKS end product. Whole coding regions of PUFA PKS genes canthen be expressed in host organisms (such as Escherichia coli or yeast)in combination with each other or with known PUFA PKS gene or genefragment combinations to evaluate their effect on PUFA production. Asdescribed above, activity in cell-free extracts can be used to determinefunction at desired temperatures. Isolated PUFA PKS genes can also betransformed directly into appropriate Schizochytrium or other suitablestrains to measure function. PUFA PKS system-encoding constructsidentified or produced in such a manner, including hybrid constructs,can also be used to transform other organisms, such as plants.

Therefore, using the non-bacterial PUFA PKS systems of the presentinvention, which, for example, makes use of genes from ThraustochytridPUFA PKS systems, as well as PUFA PKS systems and PKS systems frombacteria, gene mixing can be used to extend the range of PUFA productsto include EPA, DHA, ARA, GLA, SDA and others (described in detailbelow), as well as to produce a wide variety of bioactive molecules,including antibiotics, other pharmaceutical compounds, and otherdesirable products. The method to obtain these bioactive moleculesincludes not only the mixing of genes from various organisms but alsovarious methods of genetically modifying the non-bacterial PUFA PKSgenes disclosed herein. Knowledge of the genetic basis and domainstructure of the non-bacterial PUFA PKS system of the present inventionprovides a basis for designing novel genetically modified organismswhich produce a variety of bioactive molecules. Although mixing andmodification of any PKS domains and related genes are contemplated bythe present inventors, by way of example, various possible manipulationsof the PUFA-PKS system are discussed below with regard to geneticmodification and bioactive molecule production.

Accordingly, encompassed by the present invention are methods togenetically modify microbial or plant cells by: genetically modifying atleast one nucleic acid sequence in the organism that encodes an aminoacid sequence having the biological activity of at least one functionaldomain of a non-bacterial PUFA PKS system according to the presentinvention, and/or expressing at least one recombinant nucleic acidmolecule comprising a nucleic acid sequence encoding such amino acidsequence. Various embodiments of such sequences, methods to geneticallymodify an organism, and specific modifications have been described indetail above. Typically, the method is used to produce a particulargenetically modified organism that produces a particular bioactivemolecule or molecules.

One embodiment of the present invention relates to a geneticallymodified Thraustochytrid microorganism, wherein the microorganism has anendogenous polyunsaturated fatty acid (PUFA) polyketide synthase (PKS)system, and wherein the endogenous PUFA PKS system has been geneticallymodified to alter the expression profile of a polyunsaturated fatty acid(PUFA) by the microorganism as compared to the Thraustochytridmicroorganism in the absence of the modification. Thraustochytridmicroorganisms useful as host organisms in the present inventionendogenously contain and express a PUFA PKS system. The geneticmodification can be a genetic modification of one or more of thefunctional domains of the endogenous PUFA PKS system, whereby themodification alters the PUFA production profile of the endogenous PUFAPKS system. In addition, or as an alternative, the genetic modificationcan be an introduction of at least one exogenous nucleic acid sequence(e.g., a recombinant nucleic acid molecule) to the microorganism,wherein the exogenous nucleic acid sequence encodes at least onebiologically active domain or protein from a second PKS system and/or aprotein that affects the activity of the PUFA PKS system (e.g., aphosphopantetheinyl transferases (PPTase)). The second PKS system can beany PKS system, including other PUFA PKS systems and includinghomologues of genes from the Thraustochytrid PUFA PKS system to begenetically modified.

This embodiment of the invention is particularly useful for theproduction of commercially valuable lipids enriched in a desired PUFA,such as EPA, via the present inventors' development of geneticallymodified microorganisms and methods for efficiently producing lipids(triacylglyerols (TAG) as well as membrane-associated phospholipids(PL)) enriched in PUFAs.

This particular embodiment of the present invention is derived in partfrom the following knowledge: (1) utilization of the inherent TAGproduction capabilities of selected microorganisms, and particularly, ofThraustochytrids, such as the commercially developed Schizochytriumstrain described herein; (2) the present inventors' detailedunderstanding of PUFA PKS biosynthetic pathways (i.e., PUFA PKS systems)in eukaryotes and in particular, in members of the orderThraustochytriales; and, (3) utilization of a homologous geneticrecombination system in Schizochytrium. Based on the inventors'knowledge of the systems involved, the same general approach may beexploited to produce PUFAs other than EPA.

In one embodiment of the invention, the endogenous Thraustochytrid PUFAPKS genes, such as the Schizochytrium genes encoding PUFA PKS enzymesthat normally produce DHA and DPA, are modified by random or targetedmutagenesis, replaced with genes from other organisms that encodehomologous PKS proteins (e.g., from bacteria or other sources), orreplaced with genetically modified Schizochytrium, Thraustochytrium orother Thraustochytrid PUFA PKS genes. The product of the enzymes encodedby these introduced and/or modified genes can be EPA, for example, or itcould be some other related molecule, including other PUFAs. One featureof this method is the utilization of endogenous components ofThraustochytrid PUFA synthesis and accumulation machinery that isessential for efficient production and incorporation of the PUFA into PLand TAG. In particular, this embodiment of the invention is directed tothe modification of the type of PUFA produced by the organism, whileretaining the high oil productivity of the parent strain.

Although some of the following discussion uses the organismSchizochytrium as an exemplary host organism, any Thraustochytrid can bemodified according to the present invention, including members of thegenera Thraustochytrium, Labyrinthuloides, and Japonochytrium. Forexample, the genes encoding the PUFA PKS system for a species ofThraustochytrium have been identified (see Example 6), and this organismcan also serve as a host organism for genetic modification using themethods described herein, although it is more likely that theThraustochytrium PKS genes will be used to modify the endogenous PUFAPKS genes of another Thraustochytrid, such as Schizochytrium.Furthermore, using methods for screening organisms as set forth in U.S.application Ser. No. 10/124,800, supra, one can identify other organismsuseful in the present method and all such organisms are encompassedherein.

This embodiment of the present invention can be illustrated as follows.By way of example, based on the present inventors' current understandingof PUFA synthesis and accumulation in Schizochytrium, the overallbiochemical process can be divided into three parts.

First, the PUFAs that accumulate in Schizochytrium oil (DHA and DPA) arethe product of a PUFA PKS system as discussed above. The PUFA PKS systemin Schizochytrium converts malonyl-CoA into the end product PUFA withoutrelease of significant amounts of intermediate compounds. InSchizochytrium, three genes have been identified (Orfs A, B and C; alsorepresented by SEQ ID NO:1, SEQ ID NO:3 and SEQ ID NO:5, respectively)that encode all of the enzymatic domains known to be required for actualsynthesis of PUFAs. Similar sets of genes (encoding proteins containinghomologous sets of enzymatic domains) have been cloned and characterizedfrom several other non-eukaryotic organisms that produce PUFAs, namely,several strains of marine bacteria. In addition, the present inventorshave identified and now sequenced PUFA PKS genes in at least one othermarine protist (Thraustochytrium strain 23B) (described in detailbelow).

The PUFA products of marine bacteria include EPA (e.g., produced byShewanella SRC2738 and Photobacter profundum) as well as DHA (Vibriomarinus, now known as Moritella marina) (described in U.S. Pat. No.6,140,486, supra; and in U.S. Pat. No. 6,566,583, supra). It is anembodiment of the invention that any PUFA PKS gene set could beenvisioned to substitute for the Schizochytrium genes described in theexample herein, as long as the physiological growth requirements of theproduction organism (e.g., Schizochytrium) in fermentation conditionswere satisfied. In particular, the PUFA-producing bacterial strainsdescribed above grow only at relatively low temperatures (typically lessthan 20° C.) which further indicates that their PUFA PKS gene productswill not function at standard growth temperatures for Schizochytrium(25-30° C.). However, the inventors have recently identified at leasttwo other marine bacteria that grow and produce EPA at standard growthtemperatures for Schizochytrium and other Thraustochytrids (see Example7). These alternate marine bacteria have been shown to possessPUFA-PKS-like genes that will serve as material for modification ofSchizochytrium and other Thraustochytrids by methods described herein.It will be apparent to those skilled in the art from this disclosurethat other currently unstudied or unidentified PUFA-producing bacteriacould also contain PUFA PKS genes useful for modification ofThraustochytrids.

Second, in addition to the genes that encode the enzymes directlyinvolved in PUFA synthesis, an “accessory” enzyme is required. The geneencodes a phosphopantetheine transferase (PPTase) that activates theacyl-carrier protein (ACP) domains present in the PUFA PKS complex.Activation of the ACP domains by addition of this co-factor is requiredfor the PUFA PKS enzyme complex to function. All of the ACP domains ofthe PUFA PKS systems identified so far show a high degree of amino acidsequence conservation and, without being bound by theory, the presentinventors believe that the PPTase of Schizochytrium and otherThraustochytrids will recognize and activate ACP domains from other PUFAPKS systems. As proof of principle that heterologous PPTases and PUFAPKS genes can function together to produce a PUFA product, the presentinventors demonstrate herein the use of two different heterologousPPTases with the PUFA PKS genes from Schizochytrium to produce a PUFA ina bacterial host cell.

Third, in Schizochytrium, the products of the PUFA PKS system areefficiently channeled into both the phospholipids (PL) andtriacylglycerols (TAG). The present inventors' data suggest that thePUFA is transferred from the ACP domains of the PKS complex to coenzymeA (CoA). As in other eukaryotic organisms, this acyl-CoA would thenserve as the substrate for the various acyl-transferases that form thePL and TAG molecules. In contrast, the data indicate that in bacteria,transfer to CoA does not occur; rather, there is a direct transfer fromthe ACP domains of the PKS complex to the acyl-transferases that formPL. The enzymatic system in Schizochytrium that transfers PUFA from ACPto CoA clearly can recognize both DHA and DPA and therefore, the presentinventors believe that it is predictable that any PUFA product of thePUFA PKS system (as attached to the PUFA PKS ACP domains) will serve asa substrate.

Therefore, in one embodiment of the present invention, the presentinventors propose to alter the genes encoding the components of the PUFAPKS enzyme complex (part 1) while utilizing the endogenous PPTase fromSchizochytrium or another Thraustochytrid host (part 2) and PUFA-ACP toPUFA-CoA transferase activity and TAG/PL synthesis systems (or otherendogenous PUFA ACP to TAG/PL mechanism) (part 3). These methods of thepresent invention are supported by experimental data, some of which arepresented in the Examples section in detail.

First, the present inventors have found that the PUFA PKS system can betransferred between organisms, and that some parts are interchangeable.More particularly, it has been previously shown that the PUFA PKSpathways of the marine bacteria, Shewanella SCR2738 (Yazawa, 1996,Lipids 31:S297-300) and Vibrio marinus (along with the PPTase fromShewanella) (U.S. Pat. No. 6,140,486), can be successfully transferredto a heterologous host (i.e., to E. coli). Additionally, the degree ofstructural homology between the subunits of the PUFA PKS enzymes fromthese two organisms (Shewanella SCRC2738 and Vibrio marinus) is suchthat it has been possible to mix and match genes from the two systems(U.S. Pat. No. 6,140,486, supra). The PUFA end product of the mixed setsof genes varied depending on the origins of the specific genehomologues. At least one open reading frame (Shewanella's Orf 7 and itsVibrio marinus homologue; see FIG. 13 of U.S. Pat. No. 6,140,486; notethat the nomenclature for this Orf has changed; it is labeled as Orf 8in the patent, but was submitted to Genbank as Orf 7, and is nowreferred to by its GenBank designation) could be associated withdetermination of whether DHA or EPA would be the product of thecomposite system. The functional domains of all of the PUFA PKS enzymesidentified so far show sequence homology to one another. Similarly,these data indicated that PUFA PKS systems, including those from themarine bacteria, can be transferred to, and will function in,Schizochytrium and other Thraustochytrids.

The present inventors have now expressed the PUFA PKS genes (Orfs A, Band C) from Schizochytrium in an E. coli host and have demonstrated thatthe cells made DHA and DPA in about the same ratio as the endogenousproduction of these PUFAs in Schizochytrium (see Example 2). Therefore,it has been demonstrated that the recombinant Schizochytrium PUFA PKSgenes encode a functional PUFA synthesis system. Additionally, all orportions of the Thraustochytrium 23B OrfA and OrfC genes have been shownto function in Schizochytrium (see Example 6).

Second, the present inventors have previously found that PPTases canactivate heterologous PUFA PKS ACP domains. Production of DHA in E. colitransformed with the PUFA PKS genes from Vibrio marinus occurred onlywhen an appropriate PPTase gene (in this case, from Shewanella SCRC2738)was also present (see U.S. Pat. No. 6,140,486, supra). This demonstratedthat the Shewanella PPTase was able to activate the Vibrio PUFA PKS ACPdomains. Additionally, the present inventors have now demonstrated theactivation (pantetheinylation) of ACP domains from Schizochytrium Orf Ausing a PPTase (sfp) from Bacillus subtilus (see Example 2). The presentinventors have also demonstrated activation (pantetheinylation) of ACPdomains from Schizochytrium Orf A by a PPTase called Het I from Nostoc(see Example 2). The HetI enzyme was additionally used as the PPTase inthe experiments discussed above for the production of DHA and DPA in E.coli using the recombinant Schizochytrium PUFA PKS genes (Example 2).

Third, data indicate that DHA-CoA and DPA-CoA may be metabolicintermediates in the Schizochytrium TAG and PL synthesis pathway.Published biochemical data suggest that in bacteria, the newlysynthesized PUFAs are transferred directly from the PUFA PKS ACP domainsto the phospholipid synthesis enzymes. In contrast, the presentinventors' data indicate that in Schizochytrium, a eukaryotic organism,there may be an intermediate between the PUFA on the PUFA PKS ACPdomains and the target TAG and PL molecules. The typical carrier offatty acids in the eukaryotic cytoplasm is CoA. The inventors examinedextracts of Schizochytrium cells and found significant levels ofcompounds that co-migrated during HPLC fractionation with authenticstandards of DHA-CoA, DPA-CoA, 16:0-CoA and 18:1-CoA. The identity ofthe putative DHA-CoA and DPA-CoA peaks were confirmed using massspectroscopy. In contrast, the inventors were not able to detect DHA-CoAin extracts of Vibrio marinus, again suggesting that a differentmechanism exists in bacteria for transfer of the PUFA to its finaltarget (e.g., direct transfer to PL). The data indicate a mechanismlikely exists in Schizochytrium for transfer of the newly synthesizedPUFA to CoA (probably via a direct transfer from the ACP to CoA). BothTAG and PL synthesis enzymes could then access this PUFA-CoA. Theobservation that both DHA and DPA CoA are produced suggests that theenzymatic transfer machinery may recognize a range of PUFAs.

Fourth, the present inventors have now created knockouts of Orf A, OrfB, and Orf C in Schizochytrium (see Example 3). The knockout strategyrelies on the homologous recombination that has been demonstrated tooccur in Schizochytrium (see U.S. patent application Ser. No.10/124,807, supra). Several strategies can be employed in the design ofknockout constructs. The specific strategy used to inactivate thesethree genes utilized insertion of a Zeocin™ resistance gene coupled to atubulin promoter (derived from pMON50000, see U.S. patent applicationSer. No. 10/124,807) into a cloned portion of the Orf. The new constructcontaining the interrupted coding region was then used for thetransformation of wild type Schizochytrium cells via particlebombardment (see U.S. patent application Ser. No. 10/124,807). Bombardedcells were spread on plates containing both Zeocin™ and a supply of PUFA(see below). Colonies that grew on these plates were then streaked ontoZeocin™ plates that were not supplemented with PUFAs. Those coloniesthat required PUFA supplementation for growth were candidates for havinghad the PUFA PKS Orf inactivated via homologous recombination. In allthree cases, this presumption was confirmed by rescuing the knockout bytransforming the cells with a full-length genomic DNA clones of therespective Schizochytrium Orfs. Furthermore, in some cases, it was foundthat the Zeocin™ resistance gene had been removed (see Example 5),indicating that the introduced functional gene had integrated into theoriginal site by double homologous recombination (i.e. deleting theresistance marker). One key to the success of this strategy wassupplementation of the growth medium with PUFAs. In the present case, aneffective means of supplementation was found to be sequestration of thePUFA by mixing with partially methylated beta-cyclodextrin prior toadding to the growth medium (see Example 5). Together, these experimentsdemonstrate the principle that one of skill in the art, given theguidance provided herein, can inactivate one or more of the PUFA PKSgenes in a PUFA PKS-containing microorganism such as Schizochytrium, andcreate a PUFA auxotroph which can then be used for further geneticmodification (e.g., by introducing other PKS genes) according to thepresent invention (e.g., to alter the fatty acid profile of therecombinant organism).

One important element of the genetic modification of the organisms ofthe present invention is the ability to directly transform aThraustochytrid genome. In U.S. application Ser. No. 10/124,807, supra,transformation of Schizochytrium via single crossover homologousrecombination and targeted gene replacement via double crossoverhomologous recombination were demonstrated. As discussed above, thepresent inventors have now used this technique for homologousrecombination to inactivate Orf A, Orf B and OrfC of the PUFA-PKA systemin Schizochytrium. The resulting mutants are dependent onsupplementation of the media with PUFA. Several markers oftransformation, promoter elements for high level expression ofintroduced genes and methods for delivery of exogenous genetic materialhave been developed and are available. Therefore, the tools are in placefor knocking out endogenous PUFA PKS genes in Thraustochytrids and othereukaryotes having similar PUFA PKS systems and replacing them with genesfrom other organisms (or with modified Schizochytrium genes) as proposedabove.

In one approach for production of EPA-rich TAG, the PUFA PKS system ofSchizochytrium can be altered by the addition of heterologous genesencoding a PUFA PKS system whose product is EPA. It is anticipated thatthe endogenous PPTase will activate the ACP domains of that heterologousPUFA PKS system. Additionally, it is anticipated that the EPA will beconverted to EPA-CoA and will readily be incorporated intoSchizochytrium TAG and PL membranes. In one modification of thisapproach, techniques can be used to modify the relevant domains of theendogenous Schizochytrium system (either by introduction of specificregions of heterologous genes or by mutagenesis of the Schizochytriumgenes themselves) such that its end product is EPA rather than DHA andDPA. This is an exemplary approach, as this technology can be applied tothe production of other PUFA end products and to any eukaryoticmicroorganism that comprises a PUFA PKS system and that has the abilityto efficiently channel the products of the PUFA PKS system into both thephospholipids (PL) and triacylglycerols (TAG). In particular, theinvention is applicable to any Thraustochytrid microorganism or anyother eukaryote that has an endogenous PUFA PKS system, which isdescribed in detail below by way of example. In addition, the inventionis applicable to any suitable host organism, into which the modifiedgenetic material for production of various PUFA profiles as describedherein can be transformed. For example, in the Examples, the PUFA PKSsystem from Schizochytrium is transformed into an E. coli. Such atransformed organism could then be further modified to alter the PUFAproduction profile using the methods described herein.

The present invention can make use of genes and nucleic acid sequenceswhich encode proteins or domains from PKS systems other than the PUFAPKS system described herein and in U.S. patent application Ser. No.10/124,800, and include genes and nucleic acid sequences from bacterialand non-bacterial PKS systems, including PKS systems of Type II, Type Iand modular, described above. Organisms which express each of thesetypes of PKS systems are known in the art and can serve as sources fornucleic acids useful in the genetic modification process of the presentinvention.

In a preferred embodiment, genes and nucleic acid sequences which encodeproteins or domains from PKS systems other than the PUFA PKS system orfrom other PUFA PKS systems are isolated or derived from organisms whichhave preferred growth characteristics for production of PUFAs. Inparticular, it is desirable to be able to culture the geneticallymodified Thraustochytrid microorganism at temperatures greater thanabout 15° C., greater than 20° C., greater than 25° C., greater than 30°C., greater than 35° C., greater than 40° C., or in one embodiment, atany temperature between about 20° C. and 40° C. Therefore, PKS proteinsor domains having functional enzymatic activity at these temperaturesare preferred. For example, the present inventors describe herein theuse of PKS genes from Shewanella olleyana or Shewanella japonica, whichare marine bacteria that naturally produce EPA and grow at temperaturesup to 30° C. and 35° C., respectively (see Example 7). PKS proteins ordomains from these organisms are examples of proteins and domains thatcan be mixed with Thraustochytrid PUFA PKS proteins and domains asdescribed herein to produce a genetically modified organism that has aspecifically designed or modified PUFA production profile.

In another preferred embodiment, the genes and nucleic acid sequencesthat encode proteins or domains from a PUFA PKS system that produces onefatty acid profile are used to modify another PUFA PKS system andthereby alter the fatty acid profile of the host. For example,Thraustochytrium 23B (ATCC 20892) is significantly different fromSchizochytrium sp. (ATCC 20888) in its fatty acid profile.Thraustochytrium 23B can have DHA:DPA(n-6) ratios as high as 40:1compared to only 2-3:1 in Schizochytrium (ATCC 20888). Thraustochytrium23B can also have higher levels of C20:5(n-3). However, Schizochytrium(ATCC 20888) is an excellent oil producer as compared toThraustochytrium 23B. Schizochytrium accumulates large quantities oftriacylglycerols rich in DHA and docosapentaenoic acid (DPA; 22:5ω6);e.g., 30% DHA+DPA by dry weight. Therefore, the present inventorsdescribe herein the modification of the Schizochytrium endogenous PUFAPKS system with Thraustochytrium 23B PUFA PKS genes to create agenetically modified Schizochytrium with a DHA:DPA profile more similarto Thraustochytrium 23B (i.e., a “super-DHA-producer” Schizochytrium,wherein the production capabilities of the Schizochytrium combine withthe DHA:DPA ratio of Thraustochytrium).

Therefore, the present invention makes use of genes from ThraustochytridPUFA PKS systems, and further utilizes gene mixing to extend and/oralter the range of PUFA products to include EPA, DHA, DPA, ARA, GLA, SDAand others. The method to obtain these altered PUFA production profilesincludes not only the mixing of genes from various organisms into theThrasustochytrid PUFA PKS genes, but also various methods of geneticallymodifying the endogenous Thraustochytrid PUFA PKS genes disclosedherein. Knowledge of the genetic basis and domain structure of theThraustochytrid PUFA PKS system of the present invention (e.g.,described in detail for Schizochytrium above) provides a basis fordesigning novel genetically modified organisms which produce a varietyof PUFA profiles. Novel PUFA PKS constructs prepared in microorganismssuch as a Thraustochytrid can be isolated and used to transform plantsto impart similar PUFA production properties onto the plants.

Any one or more of the endogenous Thraustochytrid PUFA PKS domains canbe altered or replaced according to the present invention, provided thatthe modification produces the desired result (i.e., alteration of thePUFA production profile of the microorganism). Particularly preferreddomains to alter or replace include, but are not limited to, any of thedomains corresponding to the domains in Schizochytrium OrfB or OrfC(β-keto acyl-ACP synthase (KS), acyltransferase (AT), FabA-likeβ-hydroxy acyl-ACP dehydrase (DH), chain length factor (CLF), enoylACP-reductase (ER), an enzyme that catalyzes the synthesis oftrans-2-acyl-ACP, an enzyme that catalyzes the reversible isomerizationof trans-2-acyl-ACP to cis-3-acyl-ACP, and an enzyme that catalyzes theelongation of cis-3-acyl-ACP to cis-5-β-keto-acyl-ACP). In oneembodiment, preferred domains to alter or replace include, but are notlimited to, β-keto acyl-ACP synthase (KS), FabA-like β-hydroxy acyl-ACPdehydrase (DH), and chain length factor (CLF).

In one aspect of the invention, Thraustochytrid PUFA-PKS PUFA productionis altered by modifying the CLF (chain length factor) domain. Thisdomain is characteristic of Type II (dissociated enzymes) PKS systems.Its amino acid sequence shows homology to KS (keto synthase pairs)domains, but it lacks the active site cysteine. CLF may function todetermine the number of elongation cycles, and hence the chain length,of the end product. In this embodiment of the invention, using thecurrent state of knowledge of FAS and PKS synthesis, a rational strategyfor production of ARA by directed modification of the non-bacterialPUFA-PKS system is provided. There is controversy in the literatureconcerning the function of the CLF in PKS systems (Bisang et al., Nature401, 502 (1999); Yi et al., J. Am. Chem. Soc. 125, 12708 (2003)) and itis realized that other domains may be involved in determination of thechain length of the end product. However, it is significant thatSchizochytrium produces both DHA (C22:6, ω-3) and DPA (C22:5, ω-6). Inthe PUFA-PKS system the cis double bonds are introduced during synthesisof the growing carbon chain. Since placement of the ω-3 and ω-6 doublebonds occurs early in the synthesis of the molecules, one would notexpect that they would affect subsequent end-product chain lengthdetermination. Thus, without being bound by theory, the presentinventors believe that introduction of a factor (e.g. CLF) that directssynthesis of C20 units (instead of C22 units) into the SchizochytriumPUFA-PKS system will result in the production of EPA (C20:5, ω-3) andARA (C20:4, ω-6). For example, in heterologous systems, one couldexploit the CLF by directly substituting a CLF from an EPA producingsystem (such as one from Photobacterium, or preferably from amicroorganism with the preferred growth requirements as described below)into the Schizochytrium gene set. The fatty acids of the resultingtransformants can then be analyzed for alterations in profiles toidentify the transformants producing EPA and/or ARA.

By way of example, in this aspect of the invention, one could constructa clone with the CLF of OrfB replaced with a CLF from a C20 PUFA-PKSsystem. A marker gene could be inserted downstream of the coding region.More specifically, one can use the homologous recombination system fortransformation of Thraustochytrids as described herein and in detail inU.S. patent application Ser. No. 10/124,807, supra. One can thentransform the wild type Thraustochytrid cells (e.g., Schizochytriumcells), select for the marker phenotype, and then screen for those thathad incorporated the new CLF. Again, one would analyze thesetransformants for any effects on fatty acid profiles to identifytransformants producing EPA and/or ARA. If some factor other than thoseassociated with the CLF is found to influence the chain length of theend product, a similar strategy could be employed to alter thosefactors.

In another aspect of the invention, modification or substitution of theβ-hydroxy acyl-ACP dehydrase/keto synthase pairs is contemplated. Duringcis-vaccenic acid (C18:1, Δ11) synthesis in E. coli, creation of the cisdouble bond is believed to depend on a specific DH enzyme, β-hydroxyacyl-ACP dehydrase, the product of the fabA gene. This enzyme removesHOH from a β-keto acyl-ACP and leaves a trans double bond in the carbonchain. A subset of DH's, FabA-like, possess cis-trans isomerase activity(Heath et al., 1996, supra). A novel aspect of bacterial andnon-bacterial PUFA-PKS systems is the presence of two FabA-like DHdomains. Without being bound by theory, the present inventors believethat one or both of these DH domains will possess cis-trans isomeraseactivity (manipulation of the DH domains is discussed in greater detailbelow).

Another aspect of the unsaturated fatty acid synthesis in E. coli is therequirement for a particular KS enzyme, β-ketoacyl-ACP synthase, theproduct of the fabB gene. This is the enzyme that carries outcondensation of a fatty acid, linked to a cysteine residue at the activesite (by a thio-ester bond), with a malonyl-ACP. In the multi-stepreaction, CO₂ is released and the linear chain is extended by twocarbons. It is believed that only this KS can extend a carbon chain thatcontains a double bond. This extension occurs only when the double bondis in the cis configuration; if it is in the trans configuration, thedouble bond is reduced by enoyl-ACP reductase (ER) prior to elongation(Heath et al., 1996, supra). All of the PUFA-PKS systems characterizedso far have two KS domains, one of which shows greater homology to theFabB-like KS of E. coli than the other. Again, without being bound bytheory, the present inventors believe that in PUFA-PKS systems, thespecificities and interactions of the DH (FabA-like) and KS (FabB-like)enzymatic domains determine the number and placement of cis double bondsin the end products. Because the number of 2-carbon elongation reactionsis greater than the number of double bonds present in the PUFA-PKS endproducts, it can be determined that in some extension cycles completereduction occurs. Thus the DH and KS domains can be used as targets foralteration of the DHA/DPA ratio or ratios of other long chain fattyacids. These can be modified and/or evaluated by introduction ofhomologous domains from other systems or by mutagenesis of these genefragments.

In another embodiment, the ER (enoyl-ACP reductase—an enzyme whichreduces the trans-double bond in the fatty acyl-ACP resulting in fullysaturated carbons) domains can be modified or substituted to change thetype of product made by the PKS system. For example, the presentinventors know that Schizochytrium PUFA-PKS system differs from thepreviously described bacterial systems in that it has two (rather thanone) ER domains. Without being bound by theory, the present inventorsbelieve these ER domains can strongly influence the resulting PKSproduction product. The resulting PKS product could be changed byseparately knocking out the individual domains or by modifying theirnucleotide sequence or by substitution of ER domains from otherorganisms.

In another aspect of the invention, substitution of one of the DH(FabA-like) domains of the PUFA-PKS system for a DH domain that does notposses isomerization activity is contemplated, potentially creating amolecule with a mix of cis- and trans-double bonds. The current productsof the Schizochytrium PUFA PKS system are DHA and DPA (C22:5 ω6). If onemanipulated the system to produce C20 fatty acids, one would expect theproducts to be EPA and ARA (C20:4 ω6). This could provide a new sourcefor ARA. One could also substitute domains from related PUFA-PKS systemsthat produced a different DHA to DPA ratio—for example by using genesfrom Thraustochytrium 23B (the PUFA PKS system of which is identified inU.S. patent application Ser. No. 10/124,800, supra).

Additionally, in one embodiment, one of the ER domains is altered in theThraustochytrid PUFA PKS system (e.g. by removing or inactivating) toalter the end product profile. Similar strategies could be attempted ina directed manner for each of the distinct domains of the PUFA-PKSproteins using more or less sophisticated approaches. Of course onewould not be limited to the manipulation of single domains. Finally, onecould extend the approach by mixing domains from the PUFA-PKS system andother PKS or FAS systems (e.g., type I, type II, modular) to create anentire range of new PUFA end products.

It is recognized that many genetic alterations, either random ordirected, which one may introduce into a native (endogenous, natural)PKS system, will result in an inactivation of enzymatic functions.Therefore, in order to test for the effects of genetic manipulation of aThraustochytrid PUFA PKS system in a controlled environment, one couldfirst use a recombinant system in another host, such as E. coli, tomanipulate various aspects of the system and evaluate the results. Forexample, the FabB-strain of E. coli is incapable of synthesizingunsaturated fatty acids and requires supplementation of the medium withfatty acids that can substitute for its normal unsaturated fatty acidsin order to grow (see Metz et al., 2001, supra). However, thisrequirement (for supplementation of the medium) can be removed when thestrain is transformed with a functional PUFA-PKS system (i.e. one thatproduces a PUFA product in the E. coli host—see (Metz et al., 2001,supra, FIG. 2A). The transformed FabB-strain now requires a functionalPUFA-PKS system (to produce the unsaturated fatty acids) for growthwithout supplementation. The key element in this example is thatproduction of a wide range of unsaturated fatty acid will suffice (evenunsaturated fatty acid substitutes such as branched chain fatty acids).Therefore, in another preferred embodiment of the invention, one couldcreate a large number of mutations in one or more of the PUFA PKS genesdisclosed herein, and then transform the appropriately modifiedFabB-strain (e.g. create mutations in an expression construct containingan ER domain and transform a FabB-strain having the other essentialdomains on a separate plasmid—or integrated into the chromosome) andselect only for those transformants that grow without supplementation ofthe medium (i.e., that still possessed an ability to produce a moleculethat could complement the FabB-defect).

One test system for genetic modification of a PUFA PKS is exemplified inthe Examples section. Briefly, a host microorganism such as E. coli istransformed with genes encoding a PUFA PKS system including all or aportion of a Thraustochytrid PUFA PKS system (e.g., Orfs A, B and C ofSchizochytrium) and a gene encoding a phosphopantetheinyl transferases(PPTase), which is required for the attachment of a phosphopantetheinecofactor to produce the active, holo-ACP in the PKS system. The genesencoding the PKS system can be genetically engineered to introduce oneor more modifications to the Thraustochytrid PUFA PKS genes and/or tointroduce nucleic acids encoding domains from other PKS systems into theThraustochytrid genes (including genes from non-Thraustochytridmicroorganisms and genes from different Thraustochytrid microorganisms).The PUFA PKS system can be expressed in the E. coli and the PUFAproduction profile measured. In this manner, potential geneticmodifications can be evaluated prior to manipulation of theThraustochytrid PUFA production organism.

The present invention includes the manipulation of endogenous nucleicacid molecules and/or the use of isolated nucleic acid moleculescomprising a nucleic acid sequence from a Thraustochytrid PUFA PKSsystem or a homologue thereof. In one aspect, the present inventionrelates to the modification and/or use of a nucleic acid moleculecomprising a nucleic acid sequence encoding a domain from a PUFA PKSsystem having a biological activity of at least one of the followingproteins: malonyl-CoA:ACP acyltransferase (MAT), β-keto acyl-ACPsynthase (KS), ketoreductase (KR), acyltransferase (AT), FabA-likeβ-hydroxy acyl-ACP dehydrase (DH), phosphopantetheine transferase, chainlength factor (CLF), acyl carrier protein (ACP), enoyl ACP-reductase(ER), an enzyme that catalyzes the synthesis of trans-2-acyl-ACP, anenzyme that catalyzes the reversible isomerization of trans-2-acyl-ACPto cis-3-acyl-ACP, and/or an enzyme that catalyzes the elongation ofcis-3-acyl-ACP to cis-5-β-keto-acyl-ACP. Preferred domains to modify inorder to alter the PUFA production profile of a host Thraustochytridhave been discussed previously herein.

The genetic modification of a Thraustochytrid microorganism according tothe present invention preferably affects the type, amounts, and/oractivity of the PUFAs produced by the microorganism, whether theendogenous PUFA PKS system is genetically modified and/or whetherrecombinant nucleic acid molecules are introduced into the organism.According to the present invention, to affect an activity of a PUFA PKSsystem, such as to affect the PUFA production profile, includes anygenetic modification in the PUFA PKS system or genes that interact withthe PUFA PKS system that causes any detectable or measurable change ormodification in any biological activity the PUFA PKS system expressed bythe organism as compared to in the absence of the genetic modification.According to the present invention, the phrases “PUFA profile”, “PUFAexpression profile” and “PUFA production profile” can be usedinterchangeably and describe the overall profile of PUFAsexpressed/produced by a microorganism. The PUFA expression profile caninclude the types of PUFAs expressed by the microorganism, as well asthe absolute and relative amounts of the PUFAs produced. Therefore, aPUFA profile can be described in terms of the ratios of PUFAs to oneanother as produced by the microorganism, in terms of the types of PUFAsproduced by the microorganism, and/or in terms of the types and absoluteor relative amounts of PUFAs produced by the microorganism.

As discussed above, while the host microorganism can include anyeukaryotic microorganism with an endogenous PUFA PKS system and theability to efficiently channel the products of the PUFA PKS system intoboth the phospholipids (PL) and triacylglycerols (TAG), the preferredhost microorganism is any member of the order Thraustochytriales,including the families Thraustochytriaceae and Labyrinthulaceae.Particularly preferred host cells for use in the present invention couldinclude microorganisms from a genus including, but not limited to:Thraustochytrium, Japonochytrium, Aplanochytrium, Elina, andSchizochytrium within the Thraustochytriaceae, and Labyrinthula,Labyrinthuloides, and Labyrinthomyxa within the Labyrinthulaceae.Preferred species within these genera include, but are not limited to:any species within Labyrinthula, including Labrinthula sp., Labyrinthulaalgeriensis, Labyrinthula cienkowskii, Labyrinthula chattonii,Labyrinthula coenocystis, Labyrinthula macrocystis, Labyrinthulamacrocystis atlantica, Labyrinthula macrocystis macrocystis,Labyrinthula magnifica, Labyrinthula minuta, Labyrinthula roscoffensis,Labyrinthula valkanovii, Labyrinthula vitellina, Labyrinthula vitellinapacifica, Labyrinthula vitellina vitellina, Labyrinthula zopfii; anyLabyrinthuloides species, including Labyrinthuloides sp.,Labyrinthuloides minuta, Labyrinthuloides schizochytrops; anyLabyrinthomyxa species, including Labyrinthomyxa sp., Labyrinthomyxapohlia, Labyrinthomyxa sauvageaui, any Aplanochytrium species, includingAplanochytrium sp. and Aplanochytrium kerguelensis; any Elina species,including Elina sp., Elina marisalba, Elina sinorifica; anyJapanochytrium species, including Japanochytrium sp., Japanochytriummarinum; any Schizochytrium species, including Schizochytrium sp.,Schizochytrium aggregatum, Schizochytrium limacinum, Schizochytriumminutum, Schizochytrium octosporum; and any Thraustochytrium species,including Thraustochytrium sp., Thraustochytrium aggregatum,Thraustochytrium arudimentale, Thraustochytrium aureum, Thraustochytriumbenthicola, Thraustochytrium globosum, Thraustochytrium kinnei,Thraustochytrium motivum, Thraustochytrium pachydermum, Thraustochytriumproliferum, Thraustochytrium roseum, Thraustochytrium striatum, Ulkeniasp., Ulkenia minuta, Ulkenia profunda, Ulkenia radiate, Ulkeniasarkariana, and Ulkenia visurgensis. Particularly preferred specieswithin these genera include, but are not limited to: any Schizochytriumspecies, including Schizochytrium aggregatum, Schizochytrium limacinum,Schizochytrium minutum; any Thraustochytrium species (including formerUlkenia species such as U. visurgensis, U. amoeboida, U. sarkariana, U.profunda, U. radiata, U. minuta and Ulkenia sp. BP-5601), and includingThraustochytrium striatum, Thraustochytrium aureum, Thraustochytriumroseum; and any Japonochytrium species. Particularly preferred strainsof Thraustochytriales include, but are not limited to: Schizochytriumsp. (S31)(ATCC 20888); Schizochytrium sp. (S8)(ATCC 20889);Schizochytrium sp. (LC-RM)(ATCC 18915); Schizochytrium sp. (SR21);Schizochytrium aggregatum (Goldstein et Belsky)(ATCC 28209);Schizochytrium limacinum (Honda et Yokochi)(IFO 32693); Thraustochytriumsp. (23B)(ATCC 20891); Thraustochytrium striatum (Schneider)(ATCC24473); Thraustochytrium aureum (Goldstein)(ATCC 34304);Thraustochytrium roseum (Goldstein)(ATCC 28210); and Japonochytrium sp.(L1)(ATCC 28207).

In one embodiment of the present invention, it is contemplated that amutagenesis program could be combined with a selective screening processto obtain a Thraustochytrid microorganism with the PUFA productionprofile of interest. The mutagenesis methods could include, but are notlimited to: chemical mutagenesis, gene shuffling, switching regions ofthe genes encoding specific enzymatic domains, or mutagenesis restrictedto specific regions of those genes, as well as other methods.

For example, high throughput mutagenesis methods could be used toinfluence or optimize production of the desired PUFA profile. Once aneffective model system has been developed, one could modify these genesin a high throughput manner. Utilization of these technologies can beenvisioned on two levels. First, if a sufficiently selective screen forproduction of a product of interest (e.g., EPA) can be devised, it couldbe used to attempt to alter the system to produce this product (e.g., inlieu of, or in concert with, other strategies such as those discussedabove). Additionally, if the strategies outlined above resulted in a setof genes that did produce the PUFA profile of interest, the highthroughput technologies could then be used to optimize the system. Forexample, if the introduced domain only functioned at relatively lowtemperatures, selection methods could be devised to permit removing thatlimitation.

In one embodiment of the present invention, a genetically modifiedThraustochytrid microorganism has an enhanced ability to synthesizedesired PUFAs and/or has a newly introduced ability to synthesize adifferent profile of PUFAs. According to the present invention, “anenhanced ability to synthesize” a product refers to any enhancement, orup-regulation, in a pathway related to the synthesis of the product suchthat the microorganism produces an increased amount of the product(including any production of a product where there was none before) ascompared to the wild-type microorganism, cultured or grown, under thesame conditions. Methods to produce such genetically modified organismshave been described in detail above.

As described above, in one embodiment of the present invention, agenetically modified microorganism or plant includes a microorganism orplant which has an enhanced ability to synthesize desired bioactivemolecules (products) or which has a newly introduced ability tosynthesize specific products (e.g., to synthesize a specificantibiotic). According to the present invention, “an enhanced ability tosynthesize” a product refers to any enhancement, or up-regulation, in apathway related to the synthesis of the product such that themicroorganism or plant produces an increased amount of the product(including any production of a product where there was none before) ascompared to the wild-type microorganism or plant, cultured or grown,under the same conditions. Methods to produce such genetically modifiedorganisms have been described in detail above.

One embodiment of the present invention is a method to produce desiredbioactive molecules (also referred to as products or compounds) bygrowing or culturing a genetically modified microorganism or plant ofthe present invention (described in detail above). Such a methodincludes the step of culturing in a fermentation medium or growing in asuitable environment, such as soil, a microorganism or plant,respectively, that has a genetic modification as described previouslyherein and in accordance with the present invention. Preferred hostcells for genetic modification related to the PUFA PKS system of theinvention are described above.

One embodiment of the present invention is a method to produce desiredPUFAs by culturing a genetically modified Thraustochytrid microorganismof the present invention (described in detail above). Such a methodincludes the step of culturing in a fermentation medium and underconditions effective to produce the PUFA(s) a Thraustochytridmicroorganism that has a genetic modification as described previouslyherein and in accordance with the present invention. An appropriate, oreffective, medium refers to any medium in which a genetically modifiedmicroorganism of the present invention, including Thraustochytrids andother microorganisms, when cultured, is capable of producing the desiredPUFA product(s). Such a medium is typically an aqueous medium comprisingassimilable carbon, nitrogen and phosphate sources. Such a medium canalso include appropriate salts, minerals, metals and other nutrients.Any microorganisms of the present invention can be cultured inconventional fermentation bioreactors. The microorganisms can becultured by any fermentation process which includes, but is not limitedto, batch, fed-batch, cell recycle, and continuous fermentation.Preferred growth conditions for Thraustochytrid microorganisms accordingto the present invention are well known in the art and are described indetail, for example, in U.S. Pat. No. 5,130,242, U.S. Pat. No.5,340,742, and U.S. Pat. No. 5,698,244, each of which is incorporatedherein by reference in its entirety.

In one embodiment, the genetically modified microorganism is cultured ata temperature of greater than about 15° C., and in another embodiment,greater than about 20° C., and in another embodiment, greater than about25° C., and in another embodiment, greater than about 30° C., and inanother embodiment, greater than about 35° C., and in anotherembodiment, greater than about 40° C., and in one embodiment, at anytemperature between about 20° C. and 40° C.

The desired PUFA(s) and/or other bioactive molecules produced by thegenetically modified microorganism can be recovered from thefermentation medium using conventional separation and purificationtechniques. For example, the fermentation medium can be filtered orcentrifuged to remove microorganisms, cell debris and other particulatematter, and the product can be recovered from the cell-free supernatantby conventional methods, such as, for example, ion exchange,chromatography, extraction, solvent extraction, phase separation,membrane separation, electrodialysis, reverse osmosis, distillation,chemical derivatization and crystallization. Alternatively,microorganisms producing the PUFA(s), or extracts and various fractionsthereof, can be used without removal of the microorganism componentsfrom the product.

Preferably, a genetically modified Thraustochytrid microorganism of theinvention produces one or more polyunsaturated fatty acids including,but not limited to, EPA (C20:5, ω-3), DHA (C22:6, ω-3), DPA (C22:5,ω-6), ARA (C20:4, ω-6), GLA (C18:3, n-6), and SDA (C18:4, n-3)). In onepreferred embodiment, a Schizochytrium that, in wild-type form, produceshigh levels of DHA and DPA, is genetically modified according to theinvention to produce high levels of EPA. As discussed above, oneadvantage of using genetically modified Thraustochytrid microorganismsto produce PUFAs is that the PUFAs are directly incorporated into boththe phospholipids (PL) and triacylglycerides (TAG).

Preferably, PUFAs are produced in an amount that is greater than about5% of the dry weight of the microorganism, and in one aspect, in anamount that is greater than 6%, and in another aspect, in an amount thatis greater than 7%, and in another aspect, in an amount that is greaterthan 8%, and in another aspect, in an amount that is greater than 9%,and in another aspect, in an amount that is greater than 10%, and so onin whole integer percentages, up to greater than 90% dry weight of themicroorganism (e.g., 15%, 20%, 30%, 40%, 50%, and any percentage inbetween).

In the method for production of desired bioactive compounds of thepresent invention, a genetically modified plant is cultured in afermentation medium or grown in a suitable medium such as soil. Anappropriate, or effective, fermentation medium has been discussed indetail above. A suitable growth medium for higher plants includes anygrowth medium for plants, including, but not limited to, soil, sand, anyother particulate media that support root growth (e.g. vermiculite,perlite, etc.) or hydroponic culture, as well as suitable light, waterand nutritional supplements which optimize the growth of the higherplant. The genetically modified plants of the present invention areengineered to produce significant quantities of the desired productthrough the activity of the PKS system that is genetically modifiedaccording to the present invention. The compounds can be recoveredthrough purification processes which extract the compounds from theplant. In a preferred embodiment, the compound is recovered byharvesting the plant. In this embodiment, the plant can be consumed inits natural state or further processed into consumable products.

Many genetic modifications useful for producing bioactive molecules willbe apparent to those of skill in the art, given the present disclosure,and various other modifications have been discussed previously herein.The present invention contemplates any genetic modification related to aPUFA PKS system as described herein which results in the production of adesired bioactive molecule.

Bioactive molecules, according to the present invention, include anymolecules (compounds, products, etc.) that have a biological activity,and that can be produced by a PKS system that comprises at least oneamino acid sequence having a biological activity of at least onefunctional domain of a non-bacterial PUFA PKS system as describedherein. Such bioactive molecules can include, but are not limited to: apolyunsaturated fatty acid (PUFA), an anti-inflammatory formulation, achemotherapeutic agent, an active excipient, an osteoporosis drug, ananti-depressant, an anti-convulsant, an anti-Heliobactor pylori drug, adrug for treatment of neurodegenerative disease, a drug for treatment ofdegenerative liver disease, an antibiotic, and a cholesterol loweringformulation. One advantage of the non-bacterial PUFA PKS system of thepresent invention is the ability of such a system to introducecarbon-carbon double bonds in the cis configuration, and moleculesincluding a double bond at every third carbon. This ability can beutilized to produce a variety of compounds.

Preferably, bioactive compounds of interest are produced by thegenetically modified microorganism in an amount that is greater thanabout 0.05%, and preferably greater than about 0.1%, and more preferablygreater than about 0.25%, and more preferably greater than about 0.5%,and more preferably greater than about 0.75%, and more preferablygreater than about 1%, and more preferably greater than about 2.5%, andmore preferably greater than about 5%, and more preferably greater thanabout 10%, and more preferably greater than about 15%, and even morepreferably greater than about 20% of the dry weight of themicroorganism. For lipid compounds, preferably, such compounds areproduced in an amount that is greater than about 5% of the dry weight ofthe microorganism. For other bioactive compounds, such as antibiotics orcompounds that are synthesized in smaller amounts, those strainspossessing such compounds at of the dry weight of the microorganism areidentified as predictably containing a novel PKS system of the typedescribed above. In some embodiments, particular bioactive molecules(compounds) are secreted by the microorganism, rather than accumulating.Therefore, such bioactive molecules are generally recovered from theculture medium and the concentration of molecule produced will varydepending on the microorganism and the size of the culture.

One embodiment of the present invention relates to a method to modify anendproduct containing at least one fatty acid, comprising adding to theendproduct an oil produced by a recombinant host cell that expresses atleast one recombinant nucleic acid molecule comprising a nucleic acidsequence encoding at least one biologically active domain of a PUFA PKSsystem. The PUFA PKS system includes any suitable bacterial ornon-bacterial PUFA PKS system described herein, including the PUFA PKSsystems from Thraustochytrium and Schizochytrium, or any PUFA PKS systemfrom bacteria that normally (i.e., under normal or natural conditions)are capable of growing and producing PUFAs at temperatures above 22° C.,such as Shewanella olleyana or Shewanella japonica.

Preferably, the endproduct is selected from the group consisting of afood, a dietary supplement, a pharmaceutical formulation, a humanizedanimal milk, and an infant formula. Suitable pharmaceutical formulationsinclude, but are not limited to, an anti-inflammatory formulation, achemotherapeutic agent, an active excipient, an osteoporosis drug, ananti-depressant, an anti-convulsant, an anti-Heliobactor pylori drug, adrug for treatment of neurodegenerative disease, a drug for treatment ofdegenerative liver disease, an antibiotic, and a cholesterol loweringformulation. In one embodiment, the endproduct is used to treat acondition selected from the group consisting of: chronic inflammation,acute inflammation, gastrointestinal disorder, cancer, cachexia, cardiacrestenosis, neurodegenerative disorder, degenerative disorder of theliver, blood lipid disorder, osteoporosis, osteoarthritis, autoimmunedisease, preeclampsia, preterm birth, age related maculopathy, pulmonarydisorder, and peroxisomal disorder.

Suitable food products include, but are not limited to, fine bakerywares, bread and rolls, breakfast cereals, processed and unprocessedcheese, condiments (ketchup, mayonnaise, etc.), dairy products (milk,yogurt), puddings and gelatin desserts, carbonated drinks, teas,powdered beverage mixes, processed fish products, fruit-based drinks,chewing gum, hard confectionery, frozen dairy products, processed meatproducts, nut and nut-based spreads, pasta, processed poultry products,gravies and sauces, potato chips and other chips or crisps, chocolateand other confectionery, soups and soup mixes, soya based products(milks, drinks, creams, whiteners), vegetable oil-based spreads, andvegetable-based drinks.

Yet another embodiment of the present invention relates to a method toproduce a humanized animal milk. This method includes the steps ofgenetically modifying milk-producing cells of a milk-producing animalwith at least one recombinant nucleic acid molecule comprising a nucleicacid sequence encoding at least one biologically active domain of a PUFAPKS system as described herein.

Methods to genetically modify a host cell and to produce a geneticallymodified non-human, milk-producing animal, are known in the art.Examples of host animals to modify include cattle, sheep, pigs, goats,yaks, etc., which are amenable to genetic manipulation and cloning forrapid expansion of a transgene expressing population. For animals,PKS-like transgenes can be adapted for expression in target organelles,tissues and body fluids through modification of the gene regulatoryregions. Of particular interest is the production of PUFAs in the breastmilk of the host animal.

The following examples are provided for the purpose of illustration andare not intended to limit the scope of the present invention.

EXAMPLES Example 1

The following example, from U.S. patent application Ser. No. 10/124,800,describes the use of the screening process of the present invention toidentify other non-bacterial organisms comprising a PUFA PKS systemaccording to the present invention.

Thraustochytrium sp. 23B (ATCC 20892) was cultured as described indetail herein.

A frozen vial of Thraustochytrium sp. 23B (ATCC 20892) was used toinoculate a 250 mL shake flask containing 50 mL of RCA medium. Theculture was shaken on a shaker table (200 rpm) for 72 hr at 25° C. RCAmedium contains the following: RCA Medium Deionized water 1000 mL ReefCrystals ® sea salts 40 g/L Glucose 20 g/L Monosodium glutamate (MSG) 20g/L Yeast extract 1 g/L PII metals* 5 mL/L Vitamin mix* 1 mL/L pH 7.0*PII metal mix and vitamin mix are same as those outlined in U.S. Pat.No. 5,130,742, incorporated herein by reference in its entirety.

25 mL of the 72 hr old culture was then used to inoculate another 250 mLshake flask containing 50 mL of low nitrogen RCA medium (10 g/L MSGinstead of 20 g/L) and the other 25 mL of culture was used to inoculatea 250 mL shake flask containing 175 mL of low-nitrogen RCA medium. Thetwo flasks were then placed on a shaker table (200 rpm) for 72 hr at 25°C. The cells were then harvested via centrifugation and dried bylyophilization. The dried cells were analyzed for fat content and fattyacid profile and content using standard gas chromatograph procedures.

The screening results for Thraustochytrium 23B under low oxygenconditions relative to high oxygen conditions were as follows: Did DHAas % FAME increase? Yes (38->44%) C14:0 + C16:0 + C16:1 greater thanabout Yes (44%) 40% TFA? No C18:3(n − 3) or C18:3(n − 6)? Yes (0%) Didfat content increase? Yes (2-fold increase) Did DHA (or other HUFAcontent increase)? Yes (2.3-fold increase)

The results, especially the significant increase in DHA content (as %FAME) under low oxygen conditions, conditions, strongly indicates thepresence of a PUFA producing PKS system in this strain ofThraustochytrium.

In order to provide additional data confirming the presence of a PUFAPKS system, a Southern blot of Thraustochytrium 23B was conducted usingPKS probes from Schizochytrium strain 20888, a strain which has alreadybeen determined to contain a PUFA producing PKS system (i.e., SEQ IDNos:1-32 described above). Fragments of Thraustochytrium 23B genomic DNAwhich are homologous to hybridization probes from PKS PUFA synthesisgenes were detected using the Southern blot technique. Thraustochytrium23B genomic DNA was digested with either ClaI or KpnI restrictionendonucleases, separated by agarose gel electrophoresis (0.7% agarose,in standard tris-acetate-EDTA buffer), and blotted to a Schleicher &Schuell Nytran Supercharge membrane by capillary transfer. Twodigoxigenin labeled hybridization probes were used—one specific for theenoyl-ACP reductase (ER) region of Schizochytrium PKS Orf B (nucleotides5012-5511 of Orf B; SEQ ID NO:3), and the other specific for a conservedregion at the beginning of Schizochytrium PKS Orf C (nucleotides 76-549of OrfC; SEQ ID NO:5).

The OrfB-ER probe detected an approximately 13 kb ClaI fragment and anapproximately 3.6 kb KpnI fragment in the Thraustochytrium 23B genomicDNA. The OrfC probe detected an approximately 7.5 kb ClaI fragment andan approximately 4.6 kb KpnI fragment in the Thraustochytrium 23Bgenomic DNA.

Finally, a recombinant genomic library, consisting of DNA fragments fromThraustochytrium 23B genomic DNA inserted into vector lambda FIX II(Stratagene), was screened using digoxigenin labeled probescorresponding to the following segments of Schizochytrium 20888 PUFA-PKSgenes: nucleotides 7385-7879 of Orf A (SEQ ID NO:1), nucleotides5012-5511 of Orf B (SEQ ID NO:3), and nucleotides 76-549 of Orf C (SEQID NO:5). Each of these probes detected positive plaques from theThraustochytrium 23B library, indicating extensive homology between theSchizochytrium PUFA-PKS genes and the genes of Thraustochytrium 23B.

These results demonstrate that Thraustochytrium 23B genomic DNA containssequences that are homologous to PKS genes from Schizochytrium 20888.

Example 2

The following example demonstrates that Schizochytrium Orfs A, B and Cencode a functional DHA/DPA synthesis enzyme via functional expressionin E. coli.

General Preparation of E. coli Transformants

The three genes encoding the Schizochytrium PUFA PKS system thatproduces DHA and DPA in Schizochytrium (Orfs A, B & C; SEQ ID NO:1, SEQID NO:3 and SEQ ID NO:5, respectively) were cloned into a single E. coliexpression vector (derived from pET21c (Novagen)). The genes aretranscribed as a single message (by the T7 RNA-polymerase), and aribosome-binding site cloned in front of each of the genes initiatestranslation. Modification of the Orf B coding sequence was needed toobtain production of a full-length Orf B protein in E. coli (see below).An accessory gene, encoding a PPTase (see below) was cloned into asecond plasmid (derived from pACYC184, New England Biolabs).

OrfB

The Orf B gene is predicted to encode a protein with a mass of ˜224 kDa.Initial attempts at expression of the gene in E. coli resulted inaccumulation of a protein with an apparent molecular mass of ˜165 kDa(as judged by comparison to proteins of known mass during SDS-PAGE).Examination of the Orf B nucleotide sequence revealed a regioncontaining 15 sequential serine codons—all of them being the TCT codon.The genetic code contains 6 different serine codons, and three of theseare used frequently in E. coli. The present inventors used fouroverlapping oligonucleotides in combination with a polymerase chainreaction protocol to resynthesize a small portion of the Orf B gene (a˜195 base pair, BspHI to SacII restriction enzyme fragment) thatcontained the serine codon repeat region. In the synthetic Orf Bfragment, a random mixture of the 3 serine codons commonly used by E.coli was used, and some other potentially problematic codons werechanged as well (i.e., other codons rarely used by E. coli). The BspHIto SacII fragment present in the original Orf B was replaced by theresynthesized fragment (to yield Orf B*) and the modified gene wascloned into the relevant expression vectors. The modified OrfB* stillencodes the amino acid sequence of SEQ ID NO:4. Expression of themodified Orf B* clone in E. coli resulted in the appearance of a ˜224kDa protein, indicating that the full-length product of OrfB wasproduced. The sequence of the resynthesized Orf B* BspHI to SacIIfragment is shown in SEQ ID NO:80. Referring to SEQ ID NO:80, thenucleotide sequence of the resynthesized BspHI to SacII region of Orf Bis shown. The BspHI restriction site and the SacII restriction site areidentified. The BspHI site starts at nucleotide 4415 of the Orf B CDS(SEQ ID NO:3) (note: there are a total of three BspHI sites in the Orf BCDS, while the SacII site is unique). The sequence of the unmodified OrfB CDS is given in GenBank Accession number AF378328 and in SEQ ID NO:3.

PPTase

The ACP domains of the Orf A protein (SEQ ID NO:2 in Schizochytrium)must be activated by addition of phosphopantetheine group in order tofunction. The enzymes that catalyze this general type of reaction arecalled phosphopantetheine transferases (PPTases). E. coli contains twoendogenous PPTases, but it was anticipated that they would not recognizethe Orf A ACP domains from Schizochytrium. This was confirmed byexpressing Orfs A, B* (see above) and C in E. coli without an additionalPPTase. In this transformant, no DHA production was detected. Theinventors tested two heterologous PPTases in the E. coli PUFA PKSexpression system: (1) sfp (derived from Bacillus subtilis) and (2) HetI (from the cyanobacterium Nostoc strain 7120).

The sfp PPTase has been well characterized and is widely used due to itsability to recognize a broad range of substrates. Based on publishedsequence information (Nakana, et al., 1992, Molecular and GeneralGenetics 232: 313-321), an expression vector for sfp was built bycloning the coding region, along with defined up- and downstreamflanking DNA sequences, into a pACYC-184 cloning vector. Theoligonucleotides: (forward; SEQ ID NO:73)CGGGGTACCCGGGAGCCGCCTTGGCTTTGT; and (reverse; SEQ ID NO:74)AAACTGCAGCCCGGGTCCAGCTGGCAGGCACCCTG,were used to amplify the region of interest from genomic B. subtilusDNA. Convenient restriction enzyme sites were included in theoligonucleotides to facilitate cloning in an intermediate, high copynumber vector and finally into the EcoRV site of pACYC184 to create theplasmid: pBR301. Examination of extracts of E. coli transformed withthis plasmid revealed the presence of a novel protein with the mobilityexpected for sfp. Co-expression of the sfp construct in cells expressingthe Orf A, B*, C proteins, under certain conditions, resulted in DHAproduction. This experiment demonstrated that sfp was able to activatethe Schizochytrium Orf A ACP domains. In addition, the regulatoryelements associated with the sfp gene were used to create an expressioncassette into which other genes could be inserted. Specifically, the sfpcoding region (along with three nucleotides immediately upstream of theATG) in pBR301 was replaced with a 53 base pair section of DNA designedso that it contains several unique (for this construct) restrictionenzyme sites. The initial restriction enzyme site in this region is NdeI(CATATG; SEQ ID NO:79). The ATG sequence embedded in this site isutilized as the initiation methionine codon for introduced genes. Theadditional restriction sites (BglLL, NotI, SmaI, PmelI, HindIII, SpeIand XhoI) were included to facilitate the cloning process. Thefunctionality of this expression vector cassette was tested by using PCRto generate a version of sfp with a NdeI site at the 5′ end and an XhoIsite at the 3′ end. This fragment was cloned into the expressioncassette and transferred into E. coli along with the Orf A, B* and Cexpression vector. Under appropriate conditions, these cells accumulatedDHA, demonstrating that a functional sfp had been produced.

To the present inventors' knowledge, Het I has not been testedpreviously in a heterologous situation. Het I is present in a cluster ofgenes in Nostoc known to be responsible for the synthesis of long chainhydroxy-fatty acids that are a component of a glyco-lipid layer presentin heterocysts of that organism. The present inventors, without beingbound by theory, believe that Het I activates the ACP domains of aprotein, Hgl E, present in that cluster. The two ACP domains of Hgl Ehave a high degree of sequence homology to the ACP domains found inSchizochytrium Orf A. The endogenous start codon of Het I has not beenidentified (there is no methionine present in the putative protein).There are several potential alternative start codons (e.g., TTG and ATT)near the 5′ end of the open reading frame. The sequence of the region ofNostoc DNA encoding the HetI gene is shown in SEQ ID NO:81. SEQ ID NO:82represents the amino acid sequence encoded by SEQ ID NO:81. Referring toSEQ ID NO:81, limit to the upstream coding region indicated by theinframe nonsense triplet (TAA) at positions 1-3 of SEQ ID NO: 81 andends with the stop codon (TGA) at positions 715-717 of SEQ ID NO:81. Nomethionine codons (ATG) are present in the sequence. Potentialalternative initiation codons are: 3 TTG codons (positions 4-6, 7-9 and49-51 of SEQ ID NO:81), ATT (positions 76-78 of SEQ ID NO:81) and GTG(positions 235-237 of SEQ ID NO:81). A Het I expression construct wasmade by using PCR to replace the furthest 5′ potential alternative startcodon (TTG) with a methionine codon (ATG, as part of the above describedNdeI restriction enzyme recognition site), and introducing an XhoI siteat the 3′ end of the coding sequence. The modified HetI coding sequencewas then inserted into the NdeI and XhoI sites of the pACYC184 vectorconstruct containing the sfp regulatory elements. Expression of this HetI construct in E. coli resulted in the appearance of a new protein ofthe size expected from the sequence data. Co-expression of Het I withSchizochytrium Orfs A, B*, C in E. coli under several conditionsresulted in the accumulation of DHA and DPA in those cells. In all ofthe experiments in which sfp and Het I were compared, more DHA and DPAaccumulated in the cells containing the Het I construct than in cellscontaining the sfp construct.

Production of DHA and DPA in E. coli Transformants

The two plasmids encoding: (1) the Schizochytrium PUFA PKS genes (OrfsA, B* and C) and (2) the PPTase (from sfp or from Het I) weretransformed into E. coli strain BL21 which contains an inducible T7 RNApolymerase gene. Synthesis of the Schizochytrium proteins was induced byaddition of IPTG to the medium, while PPTase expression was controlledby a separate regulatory element (see above). Cells were grown undervarious defined conditions and using either of the two heterologousPPTase genes. The cells were harvested and the fatty acids wereconverted to methyl-esters (FAME) and analyzed using gas-liquidchromatography.

Under several conditions, DHA and DPA were detected in E. coli cellsexpressing the Schizochytrium PUFA PKS genes, plus either of the twoheterologous PPTases. No DHA or DPA was detected in FAMEs prepared fromcontrol cells (i.e., cells transformed with a plasmid lacking one of theOrfs). The ratio of DHA to DPA observed in E. coli approximates that ofthe endogenous DHA and DPA production observed in Schizochytrium. Thehighest level of PUFA (DHA plus DPA), representing ˜17% of the totalFAME, was found in cells grown at 32° C. in 765 medium (recipe availablefrom the American Type Culture Collection) supplemented with 10% (byweight) glycerol. Note that PUFA accumulation was also observed whencells were grown in Luria Broth supplemented with 5 or 10% glycerol, andwhen grown at 20° C. Selection for the presence of the respectiveplasmids was maintained by inclusion of the appropriate antibioticsduring the growth and IPTG (to a final concentration of 0.5 mM) was usedto induce expression of Orfs A, B* and C.

FIG. 4 shows an example chromatogram from gas-liquid chromatographicanalysis of FAMEs derived from control cells and from cells expressingthe Schizochytrium PUFA PKS genes plus a PPTase (in this case Het I).Identity of the labeled FAMEs has been confirmed using massspectroscopy.

Example 3

The following example shows demonstrates that genes encoding theSchizochytrium PUFA PKS enzyme complex can be selectively inactivated(knocked out), and that it is a lethal phenotype unless the medium issupplemented with polyunsaturated fatty acids.

Homologous recombination has been demonstrated in Schizochytrium (seecopending U.S. patent application Ser. No. 10/124,807, incorporatedherein by reference in its entirety). A plasmid designed to inactivateSchizochytrium Orf A (SEQ ID NO:1) was made by inserting a Zeocin™resistance marker into the Sma I site of a clone containing the Orf Acoding sequence. The Zeocin™ resistance marker was obtained from theplasmid pMON50000—expression of the Zeocin™ resistance gene is driven bya Schizochytrium derived tubulin promoter element (see U.S. patentapplication Ser. No. 10/124,807, ibid.). The knock-out construct thusconsists of: 5′ Schizochytrium Orf A coding sequence, the tub-Zeocin™resistance element and 3′ Schizochytrium Orf A coding sequence, allcloned into pBluescript II SK (+) vector (Stratagene).

The plasmid was introduced into Schizochytrium cells by particlebombardment and transformants were selected on plates containing Zeocin™and supplemented with polyunsaturated fatty acids (PUFA) (see Example4). Colonies that grew on the Zeocin™ plus PUFA plates were tested forability to grow on plates without the PUFA supplementation and severalwere found that required the PUFA. These PUFA auxotrophs are putativeOrf A knockouts. Northern blot analysis of RNA extracted from several ofthese mutants confirmed that a full-length Orf A message was notproduced in these mutants.

These experiments demonstrate that a Schizochytrium gene (e.g., Orf A)can be inactivated via homologous recombination, that inactivation ofOrf A results in a lethal phenotype, and that those mutants can berescued by supplementation of the media with PUFA.

Similar sets of experiments directed to the inactivation ofSchizochytrium Orf B (SEQ ID NO:3) and Orf C (SEQ ID NO:5) have yieldedsimilar results. That is, Orf B and Orf C can be individuallyinactivated by homologous recombination and those cells require PUFAsupplementation for growth.

Example 4

The following example shows that PUFA auxotrophs can be maintained onmedium supplemented with EPA, demonstrating that EPA can substitute forDHA in Schizochytrium.

As indicated in Example 3, Schizochytrium cells in which the PUFA PKScomplex has been inactivated required supplementation with PUFA tosurvive. Aside from demonstrating that Schizochytrium is dependent onthe products of this system for growth, this experimental system permitsthe testing of various fatty acids for their ability to rescue themutants. It was discovered that the mutant cells (in which any of thethree genes have been inactivated) grew as well on media supplementedwith EPA as they did on media supplemented with DHA. This resultindicates that, if the endogenous PUFA PKS complex which produces DHAwere replaced with one whose product was EPA, the cells would be viable.Additionally, these mutant cells could be rescued by supplementationwith either ARA or GLA, demonstrating the feasibility of producinggenetically modified Schizochytrium that produce these products. It isnoted that a preferred method for supplementation with PUFAs involvescombining the free fatty acids with partially methylatedbeta-cyclodextrin prior to addition of the PUFAs to the medium.

Example 5

The following example shows that inactivated PUFA genes can be replacedat the same site with active forms of the genes in order to restore PUFAsynthesis.

Double homologous recombination at the acetolactate synthase gene sitehas been demonstrated in Schizochytrium (see U.S. patent applicationSer. No. 10/124,807, supra). The present inventors tested this conceptfor replacement of the Schizochytrium PUFA PKS genes by transformationof a Schizochytrium Orf A knockout strain (described in Example 2) witha full-length Schizochytrium Orf A genomic clone. The transformants wereselected by their ability to grow on media without supplemental PUFAs.These PUFA prototrophs were then tested for resistance to Zeocin™ andseveral were found that were sensitive to the antibiotic. These resultsindicate that the introduced Schizochytrium Orf A has replaced theZeocin™ resistance gene in the knockout strain via double homologousrecombination. This experiment demonstrates the proof of concept forgene replacement within the PUFA PKS genes. Similar experiments forSchizochytrium Orf B and Orf C knock-outs have given identical results.

Example 6

This example shows that all or some portions of the Thraustochytrium 23BPUFA PKS genes can function in Schizochytrium.

As described in U.S. patent application Ser. No. 10/124,800 (supra), theDHA-producing protist Thraustochytrium 23B (Th. 23B) has been shown tocontain orfA, orfB, and orfC homologs. Complete genomic clones of thethree Th. 23B genes were used to transform the Schizochytrium straincontaining the cognate orf “knock-out”. Direct selection forcomplemented transformants was carried out in the absence of PUFAsupplementation. By this method, it was shown that the Th. 23B orfA andorfC genes could complement the Schizochytrium orfA and orfC knock-outstrains, respectively, to PUFA prototrophy. Complemented transformantswere found that either retained or lost Zeocin™ resistance (the markerinserted into the Schizochytrium genes thereby defining the knock-outs).The Zeocin™-resistant complemented transformants are likely to havearisen by a single cross-over integration of the entire Thraustochytriumgene into the Schizochytrium genome outside of the respective orfregion. This result suggests that the entire Thraustochytrium gene isfunctioning in Schizochytrium. The Zeocin™-sensitive complementedtransformants are likely to have arisen by double cross-over events inwhich portions (or conceivably all) of the Thraustochytrium genesfunctionally replaced the cognate regions of the Schizochytrium genesthat had contained the disruptive Zeocin™ resistance marker. This resultsuggests that a fraction of the Thraustochytrium gene is functioning inSchizochytrium.

Example 7

The following example shows that certain EPA-producing bacteria containPUFA PKS-like genes that appear to be suitable for modification ofSchizochytrium.

Two EPA-producing marine bacterial strains of the genus Shewanella havebeen shown to grow at temperatures typical of Schizochytriumfermentations and to possess PUFA PKS-like genes. Shewanella olleyana(Australian Collection of Antarctic Microorganisms (ACAM) strain number644; Skerratt et al., Int. J. Syst. Evol. Microbiol. 52, 2101 (2002))produces EPA and grows up to 30° C. Shewanella japonica (American TypeCulture Collection (ATCC) strain number BAA-316; Ivanova et al., Int. J.Syst. Evol. Microbiol. 51, 1027 (2001)) produces EPA and grows up to 35°C.

To identify and isolate the PUFA-PKS genes from these bacterial strains,degenerate PCR primer pairs for the KS-MAT region of bacterial orf5/pfaAgenes and the DH-DH region of bacterial orf7/pfaC genes were designedbased on published gene sequences for Shewanella SCRC-2738, Shewanellaoneidensis MR-1; Shewanella sp. GA-22; Photobacter profundum, andMoritella marina (see discussion above). Specifically, the primers andPCR conditions were designed as follows:

Primers for the KS/AT region; based on the following publishedsequences: Shewanella sp. SCRC-2738; Shewanella oneidensis MR-1;Photobacter profundum; Moritella marina: prRZ23 GGYATGMTGRTTGGTGAAGG(forward; SEQ ID NO:69) prRZ24 TRTTSASRTAYTGYGAACCTTG (reverse; SEQ IDNO:70)

Primers for the DH region; based on the following published sequences:Shewanella sp. GA-22; Shewanella sp. SCRC-2738; Photobacter profundum;Moritella marina: prRZ28 ATGKCNGAAGGTTGTGGCCA (forward; SEQ ID NO:71)prRZ29 CCWGARATRAAGCCRTTDGGTTG (reverse; SEQ ID NO:72)The PCR conditions (with bacterial chromosomal DNA as templates) were asfollows:

Reaction Mixture:

0.2 μM dNTPs

0.1 μM each primer

8% DMSO

250 ng chromosomal DNA

2.5 U Herculase® DNA polymerase (Stratagene)

1× Herculase® buffer

50 μL total volume

PCR Protocol: (1) 98° C. for 3 min.; (2) 98° C. for 40 sec.; (3) 56° C.for 30 sec.; (4) 72° C. for 90 sec.; (5) Repeat steps 2-4 for 29 cycles;(6) 72° C. for 10 min.; (7) Hold at 6° C.

For both primer pairs, PCR gave distinct products with expected sizesusing chromosomal DNA templates from either Shewanella olleyana orShewanella japonica. The four respective PCR products were cloned intopCR-BLUNT II-TOPO (Invitrogen) and insert sequences were determinedusing the M13 forward and reverse primers. In all cases, the DNAsequences thus obtained were highly homologous to known bacterial PUFAPKS gene regions.

The DNA sequences obtained from the bacterial PCR products were comparedwith known sequences and with PUFA PKS genes from Schizochytrium ATCC20888 in a standard Blastx search (BLAST parameters: Low Complexityfilter: On; Matrix: BLOSUM62; Word Size: 3; Gap Costs: Existance11,Extension 1 (BLAST described in Altschul, S. F., Madden, T. L.,Schääffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J.(1997) “Gapped BLAST and PSI-BLAST: a new generation of protein databasesearch programs.” Nucleic Acids Res. 25:3389-3402, incorporated hereinby reference in its entirety)).

At the amino acid level, the sequences with the greatest degree ofhomology to the Shewanella olleyana ACAM644 ketoacyl synthase/acyltransferase (KS-AT) deduced amino acid sequence encoded by SEQ ID NO:76were: Photobacter profundum pfaA (identity=70%; positives=81%);Shewanella oneidensis MR-1 “multi-domain β-ketoacyl synthase”(identity=66%; positives=77%); and Moritella marina ORF8 (identity=56%;positives=71%). The Schizochytrium sp. ATCC20888 orfA was 41% identicaland 56% positive to the deduced amino acid sequence encoded by SEQ IDNO:76.

At the amino acid level, the sequences with the greatest degree ofhomology to the Shewanella japonica ATCC BAA-316 ketoacyl synthase/acyltransferase (KS-AT) deduced amino acid sequence encoded by SEQ ID NO:78were: Shewanella oneidensis MR-1 “multi-domain β-ketoacyl synthase”(identity=67%; positives=79%); Shewanella sp. SCRC-2738 orf5(identity=69%; positives=77%); and Moritella marina ORF8 (identity=56%;positives=70%). The Schizochytrium sp. ATCC20888 orfA was 41% identicaland 55% positive to the deduced amino acid sequence encoded by SEQ IDNO:78.

At the amino acid level, the sequences with the greatest degree ofhomology to the Shewanella olleyana ACAM644 dehydrogenase (DH) deducedamino acid sequence encoded by SEQ ID NO:75 were: Shewanella sp.SCRC-2738 orf7 (identity=77%; positives=86%); Photobacter profundum pfaC(identity=72%; positives 81%); and Shewanella oneidensis MR-1“multi-domain β-ketoacyl synthase” (identity 75%; positives=83%). TheSchizochytrium sp. ATCC20888 orfC was 26% identical and 42% positive tothe deduced amino acid sequence encoded by SEQ ID NO:75.

At the amino acid level, the sequences with the greatest degree ofhomology to the Shewanella japonica ATCC BAA-316 dehydrogenase (DH)deduced amino acid sequence encoded by SEQ ID NO:77 were: Shewanella sp.SCRC-2738 orf7 (identity=77%; positives=86%); Photobacter profundum pfaC(identity=73%; positives=83%) and Shewanella oneidensis MR-1“multi-domain β-ketoacyl synthase” (identity=74%; positives=81%). TheSchizochytrium sp. ATCC20888 orfC was 27% identical and 42% positive tothe deduced amino acid sequence encoded by SEQ ID NO:77.

It is expected that the PUFA PKS gene sets from these two Shewanellastrains will provide beneficial sources of whole genes or individualdomains for the modification of Schizochytrium PUFA production. PUFA PKSgenes and the proteins and domains encoded thereby from either ofShewanella olleyana or Shewanella japonica are explicitly encompassed bythe present invention.

Example 8

This example demonstrates how the bacterial PUFA PKS gene fragmentsdescribed in Example 7 can be used to modify PUFA production inSchizochytrium.

All presently-known examples of PUFA PKS genes from bacteria exist asfour closely linked genes that contain the same domains as in thethree-gene Schizochytrium set. It is anticipated that the PUFA PKS genesfrom Shewanella olleyana and Shewanella japonica will likewise be foundin this tightly clustered arrangement. The homologous regions identifiedin Example 7 are used to isolate the PUFA PKS gene clusters from clonebanks of Sh. olleyana and Sh. japonica DNAs. Clone banks can beconstructed in bacteriophage lambda vectors, cosmid vectors, bacterialartificial chromosome (“BAC”) vectors, or by other methods known in theart. Desired clones containing bacterial PUFA PKS genes can beidentified by colony or plaque hybridization (as described in Example 1)using probes generated by PCR of the partial gene sequences of Example 7employing primers designed from these sequences. The complete DNAsequence of the new bacterial PUFA PKS gene sets are then used to designvectors for transformation of Schizochytrium strains defective in theendogenous PUFA PKS genes (e.g., see Examples 3, 5, and 6). Wholebacterial genes (coding sequences) may be used to replace wholeSchizochytrium genes (coding sequences), thus utilizing theSchizochytrium gene expression regions, and the fourth bacterial genemay be targeted to a different location within the genome.Alternatively, individual bacterial PUFA PKS functional domains may be“swapped” or exchanged with the analogous Schizochytrium domains bysimilar techniques of homologous recombination. It is understood thatthe sequence of the bacterial PUFA PKS genes or domains may have to bemodified to accommodate details of Schizochytrium codon usage, but thisis within the ability of those of skill in the art.

Each publication cited or discussed herein is incorporated herein byreference in its entirety.

While various embodiments of the present invention have been describedin detail, it is apparent that modifications and adaptations of thoseembodiments will occur to those skilled in the art. It is to beexpressly understood, however, that such modifications and adaptationsare within the scope of the present invention, as set forth in thefollowing claims.

1-114. (canceled)
 115. An isolated nucleic acid molecule comprising anucleic acid sequence encoding an amino acid sequence that is at least70% identical to SEQ ID NO:60, wherein said amino acid sequence hasFabA-like β-hydroxyacyl-ACP dehydrase activity.
 116. The isolatednucleic acid molecule of claim 115, comprising a nucleic acid sequenceencoding an amino acid sequence that is at least 90% identical to SEQ IDNO:64, wherein said amino acid sequence has FabA-like β-hydroxyacyl-ACPdehydrase activity.
 117. The isolated nucleic acid molecule of claim115, comprising a nucleic acid sequence encoding an amino acid sequencethat is at least 95% identical to SEQ ID NO:64, wherein said amino acidsequence has FabA-like β-hydroxyacyl-ACP dehydrase activity.
 118. Theisolated nucleic acid molecule of claim 115, consisting of a nucleicacid sequence encoding an amino acid sequence that is at least 95%identical to SEQ ID NO:64, wherein said amino acid sequence hasFabA-like β-hydroxyacyl-ACP dehydrase activity.
 119. The isolatednucleic acid molecule of claim 115, comprising a nucleic acid sequenceencoding an amino acid sequence that is at least 96% identical to SEQ IDNO:64, wherein said amino acid sequence has FabA-like β-hydroxyacyl-ACPdehydrase activity.
 120. The isolated nucleic acid molecule of claim115, consisting of a nucleic acid sequence encoding an amino acidsequence that is at least 96% identical to SEQ ID NO:64, wherein saidamino acid sequence has FabA-like β-hydroxyacyl-ACP dehydrase activity.121. The isolated nucleic acid molecule of claim 115, comprising anucleic acid sequence encoding an amino acid sequence that is at least97% identical to SEQ ID NO:64, wherein said amino acid sequence hasFabA-like β-hydroxyacyl-ACP dehydrase activity.
 122. The isolatednucleic acid molecule of claim 115, consisting of a nucleic acidsequence encoding an amino acid sequence that is at least 97% identicalto SEQ ID NO:64, wherein said amino acid sequence has FabA-likeβ-hydroxyacyl-ACP dehydrase activity.
 123. The isolated nucleic acidmolecule of claim 115, comprising a nucleic acid sequence encoding anamino acid sequence that is at least 98% identical to SEQ ID NO:64,wherein said amino acid sequence has FabA-like β-hydroxyacyl-ACPdehydrase activity.
 124. The isolated nucleic acid molecule of claim115, consisting of a nucleic acid sequence encoding an amino acidsequence that is at least 98% identical to SEQ ID NO:64, wherein saidamino acid sequence has FabA-like β-hydroxyacyl-ACP dehydrase activity.125. The isolated nucleic acid molecule of claim 115, comprising anucleic acid sequence encoding an amino acid sequence that is at least99% identical to SEQ ID NO:64, wherein said amino acid sequence hasFabA-like β-hydroxyacyl-ACP dehydrase activity.
 126. The isolatednucleic acid molecule of claim 115, consisting of a nucleic acidsequence encoding an amino acid sequence that is at least 99% identicalto SEQ ID NO:64, wherein said amino acid sequence has FabA-likeβ-hydroxyacyl-ACP dehydrase activity.
 127. The isolated nucleic acidmolecule of claim 115, comprising a nucleic acid sequence encoding anamino acid sequence of SEQ ID NO:64.
 128. The isolated nucleic acidmolecule of claim 115, consisting of a nucleic acid sequence encoding anamino acid sequence of SEQ ID NO:64.
 129. The isolated nucleic acidmolecule of claim 115, wherein the nucleic acid molecule comprises SEQID NO:63.
 130. The isolated nucleic acid molecule of claim 115, whereinthe nucleic acid molecule consists of SEQ ID NO:63.
 131. The isolatednucleic acid molecule of claim 115, wherein the nucleic acid moleculecomprises a nucleic acid sequence encoding SEQ ID NO:62.
 132. Theisolated nucleic acid molecule of claim 115, wherein the nucleic acidmolecule comprises the nucleic acid sequence of SEQ ID NO:61.
 133. Arecombinant nucleic acid molecule comprising the nucleic acid moleculeof claim 115 and a transcription control sequence.
 134. A recombinantplant cell that expresses the nucleic acid molecule of claim
 115. 135. Arecombinant microbial cell that expresses a recombinant vectorcomprising the nucleic acid molecule of claim 115 and a transcriptioncontrol sequence.
 136. The recombinant microbial cell of claim 135,wherein the microbial cell is a bacterium.
 137. The recombinantmicrobial cell of claim 135, wherein the microbial cell is aThraustochytriales microorganism.
 138. The recombinant microbial cell ofclaim 137, wherein the Thraustochytriales microorganism is aSchizochytrium or a Thraustochytrium.
 139. A method to produce at leastone polyunsaturated fatty acid (PUFA), comprising culturing underconditions effective to produce the PUFA, a plant cell or a microbialcell that expresses a PKS system for production of PUFAs, wherein theplant cell or microbial cell expresses a recombinant vector comprisingthe nucleic acid molecule of claim 115.